Diff of the two buildlogs: -- --- b1/build.log 2024-12-18 08:09:41.439444850 +0000 +++ b2/build.log 2024-12-18 09:42:13.067426652 +0000 @@ -1,7 +1,6 @@ -W: cgroups are not available on the host, not using them. I: pbuilder: network access will be disabled during build -I: Current time: Tue Jan 20 01:42:37 -12 2026 -I: pbuilder-time-stamp: 1768916557 +I: Current time: Wed Dec 18 22:10:54 +14 2024 +I: pbuilder-time-stamp: 1734509454 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -37,51 +36,84 @@ dpkg-source: info: applying disable_inchi_test.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2847219/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/327883/tmp/hooks/D01_modify_environment starting +debug: Running on codethink02-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Dec 18 08:11 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/327883/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/327883/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='2847219' - PS1='# ' - PS2='> ' + INVOCATION_ID=6eda45786c33448689b11230ee56fd50 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=327883 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.4CF0AfE2/pbuilderrc_7ltD --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.4CF0AfE2/b1 --logfile b1/build.log rdkit_202409.2-2.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/sbin/chroot' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.4CF0AfE2/pbuilderrc_sAIH --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.4CF0AfE2/b2 --logfile b2/build.log rdkit_202409.2-2.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink03-arm64 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2847219/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/327883/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -569,7 +601,7 @@ Get: 367 http://deb.debian.org/debian unstable/main arm64 texlive-latex-recommended all 2024.20241115-1 [8757 kB] Get: 368 http://deb.debian.org/debian unstable/main arm64 texlive-pictures all 2024.20241115-1 [17.0 MB] Get: 369 http://deb.debian.org/debian unstable/main arm64 texlive-latex-extra all 2024.20241115-1 [24.6 MB] -Fetched 396 MB in 2s (171 MB/s) +Fetched 396 MB in 4s (113 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package m4. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20085 files and directories currently installed.) @@ -1757,8 +1789,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Jan 20 13:43:53 UTC 2026. -Universal Time is now: Tue Jan 20 13:43:53 UTC 2026. +Local time is now: Wed Dec 18 08:13:33 UTC 2024. +Universal Time is now: Wed Dec 18 08:13:33 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:arm64 (1.83.0-4) ... @@ -1917,11 +1949,6 @@ Setting up pandoc (3.1.11.1+ds-2) ... Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up ssl-cert (1.1.3) ... -hostname: Name or service not known -make-ssl-cert: Could not get FQDN, using 'codethink03-arm64'. -make-ssl-cert: You may want to fix your /etc/hosts and/or DNS setup and run -make-ssl-cert: 'make-ssl-cert generate-default-snakeoil --force-overwrite' -make-ssl-cert: again. Setting up libboost-date-time1.83-dev:arm64 (1.83.0-4) ... Setting up x11proto-core-dev (2024.1-1) ... Setting up shared-mime-info (2.4-5+b1) ... @@ -2150,7 +2177,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/rdkit-202409.2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../rdkit_202409.2-2_source.changes +I: user script /srv/workspace/pbuilder/327883/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/327883/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/rdkit-202409.2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../rdkit_202409.2-2_source.changes dpkg-buildpackage: info: source package rdkit dpkg-buildpackage: info: source version 202409.2-2 dpkg-buildpackage: info: source distribution unstable @@ -2256,8 +2287,8 @@ -- Found Cairo: /usr/include/cairo -- Found Freetype: /usr/lib/aarch64-linux-gnu/libfreetype.so (found version "2.13.3") postgres: /usr/include/postgresql;/usr/include/postgresql/17/server --- Configuring done (3.7s) --- Generating done (1.0s) +-- Configuring done (6.0s) +-- Generating done (1.4s) CMake Warning: Manually-specified variables were not used by the project: @@ -2291,7 +2322,7 @@ -- Detecting CXX compile features - done -- Found PostgreSQL: /usr/lib/aarch64-linux-gnu/libpq.so (found version "17.2") postgres: /usr/include/postgresql;/usr/include/postgresql/17/server --- Configuring done (1.4s) +-- Configuring done (1.9s) -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/build-17 make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.2' @@ -2309,88 +2340,88 @@ cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/External/INCHI-API /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/External/INCHI-API /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/External/INCHI-API/CMakeFiles/inchi_support.dir/DependInfo.cmake "--color=" make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/RDGeneral /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/RDGeneral/CMakeFiles/RDGeneral.dir/DependInfo.cmake "--color=" make -f External/CoordGen/CMakeFiles/coordgen_support.dir/build.make External/CoordGen/CMakeFiles/coordgen_support.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/External/CoordGen /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/External/CoordGen 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/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/External/RingFamilies /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/External/RingFamilies /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/DependInfo.cmake "--color=" -make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/build -make -f External/GA/CMakeFiles/ga.dir/build.make External/GA/CMakeFiles/ga.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/External/CoordGen /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/External/CoordGen /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/External/CoordGen/CMakeFiles/coordgen_support.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/External/GA /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/External/GA /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/External/GA/CMakeFiles/ga.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/External/RingFamilies /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/External/RingFamilies /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/DependInfo.cmake "--color=" make -f External/INCHI-API/CMakeFiles/inchi_support.dir/build.make External/INCHI-API/CMakeFiles/inchi_support.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/External/INCHI-API && /usr/bin/cmake -E copy /build/reproducible-path/rdkit-202409.2/External/INCHI-API/python/inchi.py /build/reproducible-path/rdkit-202409.2/rdkit/Chem/inchi.py +make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' make -f External/CoordGen/CMakeFiles/coordgen_support.dir/build.make External/CoordGen/CMakeFiles/coordgen_support.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'External/CoordGen/CMakeFiles/coordgen_support.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +make[4]: Leaving directory 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDLog.cpp.o -MF CMakeFiles/RDGeneral.dir/RDLog.cpp.o.d -o CMakeFiles/RDGeneral.dir/RDLog.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/RDLog.cpp +make -f External/GA/CMakeFiles/ga.dir/build.make External/GA/CMakeFiles/ga.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' make -f Code/RDStreams/CMakeFiles/RDStreams.dir/build.make 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-DRDK_USE_STRICT_ROTOR_DEFINITION -Dhc_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hc.c.o -MF CMakeFiles/hc.dir/hc.c.o.d -o CMakeFiles/hc.dir/hc.c.o -c /build/reproducible-path/rdkit-202409.2/Code/ML/Cluster/Murtagh/hc.c -[ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/c++ 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hcdriver.c.o -MF CMakeFiles/hc.dir/hcdriver.c.o.d -o CMakeFiles/hc.dir/hcdriver.c.o -c /build/reproducible-path/rdkit-202409.2/Code/ML/Cluster/Murtagh/hcdriver.c -[ 1%] Building CXX object Code/RDGeneral/CMakeFiles/rdkitCatch.dir/catch_main.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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External/GA/CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/GA/CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o -MF CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o.d -o CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o -c /build/reproducible-path/rdkit-202409.2/External/GA/ga/IntegerStringChromosomePolicy.cpp +[ 1%] Linking C shared library ../../../../lib/libRDKithc.so +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/hc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -Wl,--dependency-file=CMakeFiles/hc.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKithc.so.1 -o ../../../../lib/libRDKithc.so.1.2024.09.2 CMakeFiles/hc.dir/hc.c.o CMakeFiles/hc.dir/hcdriver.c.o /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libRDKithc.so.1.2024.09.2 ../../../../lib/libRDKithc.so.1 ../../../../lib/libRDKithc.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' @@ -2405,130 +2436,161 @@ cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/External/GA && /usr/bin/cmake -E cmake_link_script CMakeFiles/ga.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ga.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitga.so.1 -o ../../lib/libRDKitga.so.1.2024.09.2 CMakeFiles/ga.dir/ga/StringChromosome.cpp.o CMakeFiles/ga.dir/ga/Chromosome.cpp.o CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o CMakeFiles/ga.dir/util/RandomUtil.cpp.o CMakeFiles/ga.dir/util/Util.cpp.o /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/External/GA && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitga.so.1.2024.09.2 ../../lib/libRDKitga.so.1 ../../lib/libRDKitga.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 2%] Built target ga -[ 2%] Linking CXX shared library ../../lib/libRDKitRDStreams.so -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/RDStreams && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDStreams.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/RDStreams.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDStreams.so.1 -o ../../lib/libRDKitRDStreams.so.1.2024.09.2 CMakeFiles/RDStreams.dir/streams.cpp.o /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/RDStreams && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDStreams.so.1.2024.09.2 ../../lib/libRDKitRDStreams.so.1 ../../lib/libRDKitRDStreams.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 2%] Built target RDStreams [ 2%] Linking CXX static library librdkitCatch.a cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -P CMakeFiles/rdkitCatch.dir/cmake_clean_target.cmake cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdkitCatch.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +[ 2%] Built target ga /usr/bin/ar qc librdkitCatch.a CMakeFiles/rdkitCatch.dir/catch_main.cpp.o /usr/bin/ranlib librdkitCatch.a make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 2%] Built target rdkitCatch [ 2%] Linking CXX shared library ../../lib/libRDKitRDGeneral.so cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDGeneral.dir/link.txt --verbose=1 +[ 2%] Linking CXX shared library ../../lib/libRDKitRDStreams.so +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/RDStreams && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDStreams.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/RDGeneral.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDGeneral.so.1 -o ../../lib/libRDKitRDGeneral.so.1.2024.09.2 CMakeFiles/RDGeneral.dir/Invariant.cpp.o CMakeFiles/RDGeneral.dir/types.cpp.o CMakeFiles/RDGeneral.dir/utils.cpp.o CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o CMakeFiles/RDGeneral.dir/RDLog.cpp.o CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o CMakeFiles/RDGeneral.dir/versions.cpp.o -ldl /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeneral.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1 ../../lib/libRDKitRDGeneral.so +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/RDStreams.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDStreams.so.1 -o ../../lib/libRDKitRDStreams.so.1.2024.09.2 CMakeFiles/RDStreams.dir/streams.cpp.o /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/RDStreams && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDStreams.so.1.2024.09.2 ../../lib/libRDKitRDStreams.so.1 ../../lib/libRDKitRDStreams.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 2%] Built target RDGeneral make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/depend +make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/DataStructs /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake "--color=" -make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make 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/build/reproducible-path/rdkit-202409.2/Code/Numerics/EigenSolvers /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/Numerics/EigenSolvers /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/RDBoost /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/RDBoost /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/RDBoost/CMakeFiles/RDBoost.dir/DependInfo.cmake "--color=" make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/depend +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/RDBoost /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/RDBoost /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/RDBoost/CMakeFiles/RDBoost.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/RDGeneral /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/RDGeneral/CMakeFiles/testDict.dir/DependInfo.cmake "--color=" make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/depend +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/RDGeneral /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/RDGeneral/CMakeFiles/testDict.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/RDGeneral /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/RDGeneral/CMakeFiles/testRDValue.dir/DependInfo.cmake "--color=" make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/RDGeneral /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/DependInfo.cmake "--color=" -make -f Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/RDGeneral /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/DependInfo.cmake "--color=" -make -f Code/RDGeneral/CMakeFiles/logTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/logTestsCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/RDGeneral /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/RDGeneral/CMakeFiles/logTestsCatch.dir/DependInfo.cmake "--color=" -make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/Numerics /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/Numerics /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/Numerics/CMakeFiles/testMatrices.dir/DependInfo.cmake "--color=" -make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/Catalogs /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/Catalogs /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/Catalogs/CMakeFiles/Catalogs.dir/DependInfo.cmake "--color=" -make -f Code/Query/CMakeFiles/testQuery.dir/build.make 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/build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/DataManip/MetricMatrixCalc /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build -make[4]: Leaving directory 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -MF CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o.d -o CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/DataManip/MetricMatrixCalc/testMatCalc.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 2%] Building CXX object 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-I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -MF CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o.d -o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/Catalogs/CatalogEntry.cpp [ 5%] Linking CXX shared library ../../lib/libRDKitRDBoost.so cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/RDBoost && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDBoost.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -MF CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o.d -o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/SimDivPickers/HierarchicalClusterPicker.cpp make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/RDBoost/Wrap /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/RDBoost/Wrap /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/DependInfo.cmake "--color=" @@ -2572,9 +2617,12 @@ cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/RDBoost/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdBase_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o -MF CMakeFiles/rdBase.dir/RDBase.cpp.o.d -o CMakeFiles/rdBase.dir/RDBase.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/RDBoost/Wrap/RDBase.cpp [ 5%] Linking CXX executable dictTestsCatch cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/dictTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/dictTestsCatch.dir/link.d CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o -o dictTestsCatch librdkitCatch.a ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/libCatch2.a /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 5%] Linking CXX shared library ../../lib/libRDKitCatalogs.so +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Catalogs.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 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'/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 5%] Building CXX object Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/Clustering.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DClustering_EXPORTS -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/Clustering.cpp.o -MF CMakeFiles/Clustering.dir/Clustering.cpp.o.d -o CMakeFiles/Clustering.dir/Clustering.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ML/Cluster/Murtagh/Clustering.cpp -[ 5%] Linking CXX shared library ../../lib/libRDKitCatalogs.so -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Catalogs.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o -MF CMakeFiles/DataStructs.dir/Utils.cpp.o.d -o CMakeFiles/DataStructs.dir/Utils.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Utils.cpp -[ 5%] Linking CXX executable testQuery -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/Query && /usr/bin/cmake -E cmake_link_script CMakeFiles/testQuery.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/logTestsCatch.dir/link.d CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -o logTestsCatch librdkitCatch.a ../../lib/libRDKitRDGeneral.so.1.2024.09.2 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o -MF CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o.d -o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/DataStructs/DiscreteValueVect.cpp +[ 5%] Built target testMatCalc [ 5%] Linking CXX executable testMatrices cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatrices.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -MF CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o.d -o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/DataStructs/MultiFPBReader.cpp [ 5%] Linking CXX shared library ../../lib/libRDKitSimDivPickers.so cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/SimDivPickers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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'/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/build cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/DataStructs/Wrap /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DependInfo.cmake "--color=" -make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -cd 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Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. 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../../../../rdkit/ML/Cluster/Clustering.so CMakeFiles/Clustering.dir/Clustering.cpp.o ../../../../lib/libRDKithc.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 -ldl /usr/lib/aarch64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 7%] Building CXX object Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ML/InfoTheory && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DInfoTheory_EXPORTS -DRDKIT_DYN_LINK 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CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ML/InfoTheory/InfoBitRanker.cpp +[ 7%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem 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Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -MF CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o.d -o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/DiscreteValueVect.cpp [ 8%] Linking CXX executable catchDataStructs cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/catchDataStructs.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/catchDataStructs.dir/link.d CMakeFiles/catchDataStructs.dir/catch_tests.cpp.o -o catchDataStructs ../RDGeneral/librdkitCatch.a ../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/libCatch2.a ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -2757,82 +2782,56 @@ [ 8%] Built target catchDataStructs [ 8%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -MF CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o.d -o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp -[ 8%] Linking CXX executable pickersTestsCatch -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/pickersTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pickersTestsCatch.dir/link.d CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o -o pickersTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSimDivPickers.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/libCatch2.a ../../lib/libRDKithc.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 8%] Built target pickersTestsCatch -[ 8%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/SimDivPickers/Wrap/LeaderPicker.cpp -[ 8%] Linking CXX shared library ../../lib/libRDKitRDGeometryLib.so -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDGeometryLib.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/RDGeometryLib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDGeometryLib.so.1 -o ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 CMakeFiles/RDGeometryLib.dir/point.cpp.o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1 ../../lib/libRDKitRDGeometryLib.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 8%] Built target RDGeometryLib -make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol 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../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMetricMatrixCalc.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMetricMatrixCalc.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 8%] Built target rdMetricMatrixCalc -make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/Numerics/Alignment /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu 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Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 8%] Building CXX object Code/Geometry/CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -MF CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/Geometry/catch_tests.cpp /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp: In instantiation of 'boost::python::list {anonymous}::BulkDice(const T&, boost::python::list, bool) [with T = RDKit::SparseIntVect]': /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:193:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = int]' 193 | python::def("BulkDiceSimilarity", &BulkDice>, @@ -2854,6 +2853,7 @@ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:77:48: note: the temporary was destroyed at the end of the full expression 'boost::python::extract >(boost::python::api::proxy::operator boost::python::api::object() const [with Policies = boost::python::api::item_policies]()).boost::python::extract >::boost::python::converter::extract_rvalue >.boost::python::converter::extract_rvalue >::operator()()' 77 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +[ 9%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp: In instantiation of 'boost::python::list {anonymous}::BulkTanimoto(const T&, boost::python::list, bool) [with T = RDKit::SparseIntVect]': /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:203:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = int]' 203 | python::def("BulkTanimotoSimilarity", @@ -2877,6 +2877,7 @@ /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/SparseIntVect.cpp:90:48: note: the temporary was destroyed at the end of the full expression 'boost::python::extract >(boost::python::api::proxy::operator boost::python::api::object() const [with Policies = boost::python::api::item_policies]()).boost::python::extract >::boost::python::converter::extract_rvalue >.boost::python::converter::extract_rvalue >::operator()()' 90 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK 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boost::python::api::item_policies]()).boost::python::extract >::boost::python::converter::extract_rvalue >.boost::python::converter::extract_rvalue >::operator()()' 104 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -[ 8%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/wrap_ExplicitBV.cpp -[ 8%] Linking CXX shared library ../../../lib/libRDKitAlignment.so +[ 9%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o +cd 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Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. 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CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o -MF CMakeFiles/rdGeometry.dir/Point.cpp.o.d -o CMakeFiles/rdGeometry.dir/Point.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/Geometry/Wrap/Point.cpp -[ 8%] Linking CXX executable testTransforms +[ 11%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -MF CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o.d -o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/Geometry/Wrap/UniformGrid3D.cpp +[ 11%] Linking CXX executable testTransforms cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script 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/usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 12%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include 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/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Kekulize.cpp /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolPickler.cpp: In function 'void RDKit::streamReadPositiveChar(std::istream&, char&, int)': /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolPickler.cpp:72:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 72 | if (res < 0) { | ~~~~^~~ +[ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS 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/usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +[ 14%] Built target rdGeometry [ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o -MF CMakeFiles/GraphMol.dir/AddHs.cpp.o.d -o CMakeFiles/GraphMol.dir/AddHs.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/AddHs.cpp [ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o @@ -3320,15 +3351,15 @@ cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o -MF CMakeFiles/GraphMol.dir/Conformer.cpp.o.d -o CMakeFiles/GraphMol.dir/Conformer.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Conformer.cpp [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o -MF CMakeFiles/GraphMol.dir/Renumber.cpp.o.d -o CMakeFiles/GraphMol.dir/Renumber.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Renumber.cpp -[ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o -MF CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o.d -o CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/AdjustQuery.cpp -[ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o -MF CMakeFiles/GraphMol.dir/Resonance.cpp.o.d -o CMakeFiles/GraphMol.dir/Resonance.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Resonance.cpp [ 15%] Linking CXX shared module ../../../rdkit/rdBase.so cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/RDBoost/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdBase.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdBase.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/rdBase.so CMakeFiles/rdBase.dir/RDBase.cpp.o ../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 -ldl /usr/lib/aarch64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 15%] Built target rdBase +[ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o -MF CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o.d -o CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/AdjustQuery.cpp +[ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o -MF CMakeFiles/GraphMol.dir/Resonance.cpp.o.d -o CMakeFiles/GraphMol.dir/Resonance.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Resonance.cpp [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/StereoGroup.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/StereoGroup.cpp.o -MF CMakeFiles/GraphMol.dir/StereoGroup.cpp.o.d -o CMakeFiles/GraphMol.dir/StereoGroup.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/StereoGroup.cpp [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o @@ -3355,92 +3386,98 @@ [ 16%] Built target GraphMol make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms 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directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make 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-DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o -MF CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o.d -o CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o -c 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Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build +[ 16%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/SmilesParseOps.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +[ 17%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_TRAJECTORY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DTrajectory_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o -MF CMakeFiles/Trajectory.dir/Trajectory.cpp.o.d -o CMakeFiles/Trajectory.dir/Trajectory.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Trajectory/Trajectory.cpp cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend -cd 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-DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -MF CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/SmartsWrite.cpp -[ 16%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -make[4]: Leaving directory 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/SmilesWrite.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 17%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o 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Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o -MF CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o.d -o CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/CIPLabeler.cpp +[ 19%] Linking CXX executable tableTestsCatch +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/tableTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tableTestsCatch.dir/link.d CMakeFiles/tableTestsCatch.dir/catch_periodictable.cpp.o -o tableTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitGraphMol.so.1.2024.09.2 /usr/lib/libCatch2.a ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 19%] Built target tableTestsCatch @@ -3452,12 +3489,14 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 19%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Parser.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/build/reproducible-path/rdkit-202409.2/External/rapidjson-1.1.0/include -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Parser.cpp.o -MF CMakeFiles/MolInterchange.dir/Parser.cpp.o.d -o CMakeFiles/MolInterchange.dir/Parser.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolInterchange/Parser.cpp -[ 19%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/Trajectory.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Trajectory.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTrajectory.so.1 -o ../../../lib/libRDKitTrajectory.so.1.2024.09.2 CMakeFiles/Trajectory.dir/Trajectory.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../lib/libRDKitTrajectory.so.1 ../../../lib/libRDKitTrajectory.so +[ 19%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o -MF CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o.d -o CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/CanonicalizeStereoGroups.cpp +[ 19%] Linking CXX shared library ../../../lib/libRDKitPartialCharges.so +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/PartialCharges.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/PartialCharges.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitPartialCharges.so.1 -o ../../../lib/libRDKitPartialCharges.so.1.2024.09.2 CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitPartialCharges.so.1.2024.09.2 ../../../lib/libRDKitPartialCharges.so.1 ../../../lib/libRDKitPartialCharges.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 19%] Built target Trajectory +[ 19%] Built target PartialCharges make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/DependInfo.cmake "--color=" @@ -3466,12 +3505,18 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 19%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o -MF CMakeFiles/SLNParse.dir/SLNParse.cpp.o.d -o CMakeFiles/SLNParse.dir/SLNParse.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SLNParse/SLNParse.cpp -[ 19%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolCatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolCatalog.so.1 -o ../../../lib/libRDKitMolCatalog.so.1.2024.09.2 CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolCatalog.so.1.2024.09.2 ../../../lib/libRDKitMolCatalog.so.1 ../../../lib/libRDKitMolCatalog.so +[ 19%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && 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-fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -MF CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o.d -o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/smarts.tab.cpp +[ 19%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -MF CMakeFiles/CIPLabeler.dir/Mancude.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/Mancude.cpp +[ 19%] Linking CXX shared library ../../../lib/libRDKitGenericGroups.so +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_link_script CMakeFiles/GenericGroups.dir/link.txt --verbose=1 +[ 19%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 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target GenericGroups make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/DependInfo.cmake "--color=" @@ -3480,48 +3525,44 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 19%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/rdqueries.cpp.o cd 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/rdqueries.cpp.o -MF CMakeFiles/rdqueries.dir/rdqueries.cpp.o.d -o CMakeFiles/rdqueries.dir/rdqueries.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/rdqueries.cpp -[ 19%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS 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/usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1 ../../../lib/libRDKitGenericGroups.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 20%] Built target GenericGroups +[ 19%] Built target Subgraphs make -f Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build.make Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 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Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat 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CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o.d -o CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/SubstructMatch.cpp -[ 20%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -MF CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o.d -o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/smiles.tab.cpp -[ 20%] Linking CXX shared library ../../../lib/libRDKitSubgraphs.so -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Subgraphs.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 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/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1 ../../../lib/libRDKitSubgraphs.so +[ 21%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION 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Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp +[ 22%] Linking CXX shared module ../../../rdkit/Chem/rdChemicalFeatures.so +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemicalFeatures.dir/link.txt --verbose=1 +[ 22%] Building CXX object 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-DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolTransforms_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 -ldl /usr/lib/aarch64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -[ 23%] Built target rdPartialCharges +[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 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Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat 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Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolCatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 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CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o.d -o CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Abbreviations/AbbreviationsUtils.cpp [ 24%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdqueries.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdqueries.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdqueries.so 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o -MF CMakeFiles/ForceField.dir/ForceField.cpp.o.d -o CMakeFiles/ForceField.dir/ForceField.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/ForceField.cpp +[ 25%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ 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Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -MF CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o.d -o CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/Numerics/Optimizer/testOptimizer.cpp +[ 25%] Linking CXX shared library ../../../lib/libRDKitCIPLabeler.so +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_link_script CMakeFiles/CIPLabeler.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/CIPLabeler.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitCIPLabeler.so.1 -o 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o -MF CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/DistanceConstraint.cpp -[ 24%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ForceField && 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Code/ForceField/CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/TorsionConstraint.cpp -[ 24%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SLNParse.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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/build/reproducible-path/rdkit-202409.2/Code/GraphMol/itertest.cpp -[ 25%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ShapeHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ShapeHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitShapeHelpers.so.1 -o ../../../lib/libRDKitShapeHelpers.so.1.2024.09.2 CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SLNParse.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSLNParse.so.1 -o ../../../lib/libRDKitSLNParse.so.1.2024.09.2 CMakeFiles/SLNParse.dir/SLNParse.cpp.o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o CMakeFiles/SLNParse.dir/sln.tab.cpp.o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSLNParse.so.1.2024.09.2 ../../../lib/libRDKitSLNParse.so.1 ../../../lib/libRDKitSLNParse.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 25%] Built target ShapeHelpers +[ 26%] Built target SLNParse make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol 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../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make -f Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/AngleConstraint.cpp.o -MF CMakeFiles/ForceField.dir/AngleConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/AngleConstraint.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/AngleConstraint.cpp +[ 26%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ShapeHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 26%] Linking CXX shared library ../../../lib/libRDKitReducedGraphs.so +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/ReducedGraphs.dir/link.txt --verbose=1 +[ 26%] Linking CXX shared library ../../../lib/libRDKitMolInterchange.so +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInterchange.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ReducedGraphs.dir/link.d -Wl,-z,relro -Wl,-z,now 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Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -MF CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF/AngleBend.cpp -[ 26%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 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Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF/Nonbonded.cpp -[ 27%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolCatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o 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-I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/AngleConstraints.cpp.o -MF CMakeFiles/ForceField.dir/AngleConstraints.cpp.o.d -o CMakeFiles/ForceField.dir/AngleConstraints.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/AngleConstraints.cpp +[ 27%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolCatalog.dir/link.txt 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/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/Fingerprints.cpp +[ 27%] Linking CXX executable graphmolIterTest +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolIterTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolIterTest.dir/link.d CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -o graphmolIterTest ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 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-DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/smatest.cpp.o -MF CMakeFiles/smaTest1.dir/smatest.cpp.o.d -o CMakeFiles/smaTest1.dir/smatest.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/smatest.cpp +[ 28%] Linking CXX executable moliteratorTestsCatch +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/moliteratorTestsCatch.dir/link.txt --verbose=1 +[ 28%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 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-Wl,--dependency-file=CMakeFiles/moliteratorTestsCatch.dir/link.d CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o -o moliteratorTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 /usr/lib/libCatch2.a ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +[ 28%] Built target moliteratorTestsCatch make -f Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/depend make[4]: Entering directory 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-Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule4b.cpp -[ 28%] Linking CXX executable queryTestsCatch -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/queryTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/queryTestsCatch.dir/link.d CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o -o queryTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 /usr/lib/libCatch2.a ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 28%] Built target queryTestsCatch +[ 28%] Built target MolAlign make -f Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/DependInfo.cmake "--color=" @@ -3851,11 +3967,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 28%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o -MF CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Subgraphs/catch_tests.cpp -[ 28%] Linking CXX executable molbundleTestsCatch -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molbundleTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molbundleTestsCatch.dir/link.d CMakeFiles/molbundleTestsCatch.dir/catch_molbundle.cpp.o -o molbundleTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 /usr/lib/libCatch2.a ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 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../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 28%] Built target molbundleTestsCatch +[ 28%] Built target smiTest2 make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog 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/usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 28%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/FilterCatalog.cpp +[ 28%] Linking CXX executable molopsTestsCatch +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script 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Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 28%] Built target smiTest2 +[ 28%] Built target molopsTestsCatch make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/DependInfo.cmake "--color=" @@ -3877,17 +3995,13 @@ make[4]: Entering directory 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-DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule4c.cpp -[ 28%] Linking CXX executable molopsTestsCatch -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molopsTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molopsTestsCatch.dir/link.d CMakeFiles/molopsTestsCatch.dir/catch_molops.cpp.o -o molopsTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 /usr/lib/libCatch2.a ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 28%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o -MF CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o.d -o CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/DistanceConstraints.cpp +[ 28%] Linking CXX executable molbundleTestsCatch +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molbundleTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molbundleTestsCatch.dir/link.d CMakeFiles/molbundleTestsCatch.dir/catch_molbundle.cpp.o -o molbundleTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 /usr/lib/libCatch2.a ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 28%] Built target molopsTestsCatch +[ 28%] Built target molbundleTestsCatch make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/DependInfo.cmake "--color=" @@ -3896,10 +4010,10 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 28%] Building CXX object 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o -MF CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o.d -o CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ShapeHelpers/Wrap/rdShapeHelpers.cpp -[ 29%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o -cd 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Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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'/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 31%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/c++ -DAbbreviations_EXPORTS -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_ABBREVIATIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 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Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog/FragCatGenerator.cpp -[ 31%] Linking CXX shared library ../../../lib/libRDKitCIPLabeler.so -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_link_script CMakeFiles/CIPLabeler.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/CIPLabeler.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitCIPLabeler.so.1 -o 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make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build +[ 32%] Built target rdCIPLabeler +make -f Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build.make Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 31%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolAlign_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLALIGN_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp -[ 31%] Linking CXX shared library ../../../lib/libRDKitReducedGraphs.so -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/ReducedGraphs.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ReducedGraphs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared 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Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog/FragCatParams.cpp -[ 31%] Linking CXX shared library ../../lib/libRDKitForceField.so -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceField.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ForceField.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceField.so.1 -o ../../lib/libRDKitForceField.so.1.2024.09.2 CMakeFiles/ForceField.dir/ForceField.cpp.o CMakeFiles/ForceField.dir/AngleConstraint.cpp.o CMakeFiles/ForceField.dir/AngleConstraints.cpp.o CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o CMakeFiles/ForceField.dir/PositionConstraint.cpp.o CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o CMakeFiles/ForceField.dir/UFF/Inversions.cpp.o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/UFF/Params.cpp.o CMakeFiles/ForceField.dir/UFF/Utils.cpp.o CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o ../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitForceField.so.1.2024.09.2 ../../lib/libRDKitForceField.so.1 ../../lib/libRDKitForceField.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 31%] Built target ForceField -make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make 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object Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/smatest.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/smatest.cpp.o -MF CMakeFiles/smaTest1.dir/smatest.cpp.o.d -o CMakeFiles/smaTest1.dir/smatest.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/smatest.cpp -[ 32%] Linking CXX shared module ../../../../rdkit/Chem/rdSLNParse.so +[ 33%] Built target rdMolInterchange +[ 33%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp +[ 33%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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-I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF/Nonbonded.cpp +[ 33%] Linking CXX shared module ../../../../rdkit/Chem/rdSLNParse.so cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSLNParse.dir/link.txt --verbose=1 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/usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 32%] Built target rdSLNParse -make -f Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/Wrap /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap 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-I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF/Inversion.cpp +[ 33%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversions.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -MF CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o.d -o CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ReducedGraphs/Wrap/rdReducedGraphs.cpp -[ 33%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FragCatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall 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CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.cpp -[ 33%] Linking CXX shared library ../../../lib/libRDKitMolAlign.so -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolAlign.dir/link.txt --verbose=1 -[ 33%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolChemicalFeatures/Wrap/rdMolChemicalFeatures.cpp -[ 33%] Linking CXX shared module ../../../../rdkit/Chem/rdCIPLabeler.so -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCIPLabeler.dir/link.txt --verbose=1 -[ 34%] Linking CXX executable testReducedGraphs -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReducedGraphs.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdCIPLabeler.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdCIPLabeler.so 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Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o -MF CMakeFiles/Fingerprints.dir/MHFP.cpp.o.d -o CMakeFiles/Fingerprints.dir/MHFP.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/MHFP.cpp -/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp: In function 'void RDKit::MMFF::Tools::addStretchBend(const RDKit::ROMol&, RDKit::MMFF::MMFFMolProperties*, 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-DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp +[ 35%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp +[ 35%] Linking CXX shared library ../../../lib/libRDKitDepictor.so +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/Depictor.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection 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../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDepictor.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1 ../../../lib/libRDKitDepictor.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 36%] Built target Depictor +[ 35%] Built target Depictor make -f External/INCHI-API/CMakeFiles/RDInchiLib.dir/build.make External/INCHI-API/CMakeFiles/RDInchiLib.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/External/INCHI-API /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/External/INCHI-API /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/External/INCHI-API/CMakeFiles/RDInchiLib.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' make -f External/INCHI-API/CMakeFiles/RDInchiLib.dir/build.make External/INCHI-API/CMakeFiles/RDInchiLib.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 37%] Building CXX object External/INCHI-API/CMakeFiles/RDInchiLib.dir/inchi.cpp.o +[ 36%] Building CXX object External/INCHI-API/CMakeFiles/RDInchiLib.dir/inchi.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/External/INCHI-API && /usr/bin/c++ 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Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o -MF CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o.d -o CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemTransforms/ChemTransforms.cpp -[ 37%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o +[ 36%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -c 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 36%] Linking CXX shared library ../../lib/libRDKitForceField.so +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceField.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ForceField.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceField.so.1 -o ../../lib/libRDKitForceField.so.1.2024.09.2 CMakeFiles/ForceField.dir/ForceField.cpp.o CMakeFiles/ForceField.dir/AngleConstraint.cpp.o CMakeFiles/ForceField.dir/AngleConstraints.cpp.o CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o CMakeFiles/ForceField.dir/PositionConstraint.cpp.o CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o CMakeFiles/ForceField.dir/UFF/Inversions.cpp.o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/UFF/Params.cpp.o CMakeFiles/ForceField.dir/UFF/Utils.cpp.o CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o ../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitForceField.so.1.2024.09.2 ../../lib/libRDKitForceField.so.1 ../../lib/libRDKitForceField.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 37%] Built target rdMolChemicalFeatures +[ 36%] Built target ForceField make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu 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-DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o -MF CMakeFiles/MolHash.dir/hashfunctions.cpp.o.d -o CMakeFiles/MolHash.dir/hashfunctions.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolHash/hashfunctions.cpp -[ 37%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so +[ 36%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/FilterCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFilterCatalog.so.1 -o ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 CMakeFiles/FilterCatalog.dir/Filters.cpp.o 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cmake_symlink_library ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1 ../../../lib/libRDKitFilterCatalog.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 37%] Built target FilterCatalog -make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend +[ 36%] Built target FilterCatalog +make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -MF CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o.d -o CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp -[ 38%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -MF CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o.d -o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp -[ 38%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o +[ 36%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/c++ 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-fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o -MF CMakeFiles/MolHash.dir/hashfunctions.cpp.o.d -o CMakeFiles/MolHash.dir/hashfunctions.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolHash/hashfunctions.cpp +[ 36%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemTransforms_EXPORTS -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -MF CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o.d -o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemTransforms/MolFragmenter.cpp +[ 36%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o cd 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-Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o -MF CMakeFiles/MolHash.dir/normalize.cpp.o.d -o CMakeFiles/MolHash.dir/normalize.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolHash/normalize.cpp -[ 38%] Linking CXX shared library ../../../lib/libRDKitForceFieldHelpers.so -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../lib/libRDKitForceFieldHelpers.so.1 ../../../lib/libRDKitForceFieldHelpers.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 38%] Built target ForceFieldHelpers -make -f Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/build.make Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends 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/usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -make -f Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/build.make Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/build +[ 36%] Built target rdMolChemicalFeatures +make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 38%] Building CXX object Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ 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CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/DistGeom/DistViolationContrib.cpp -make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend +make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/ForceField/Wrap /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ForceField/Wrap 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContribs.cpp.o -MF CMakeFiles/DistGeometry.dir/DistViolationContribs.cpp.o.d -o CMakeFiles/DistGeometry.dir/DistViolationContribs.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/DistGeom/DistViolationContribs.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build +make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -MF CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o.d -o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/DistGeom/ChiralViolationContrib.cpp -[ 38%] Linking CXX shared library ../../lib/libRDKitRDInchiLib.so +[ 37%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -MF CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o.d -o CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp +[ 37%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -MF CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o.d -o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemTransforms/MolFragmenter.cpp -[ 39%] Linking CXX shared module ../../../../rdkit/Chem/rdDepictor.so -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDepictor.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp +[ 40%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/Fingerprints.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Fingerprints.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFingerprints.so.1 -o ../../../lib/libRDKitFingerprints.so.1.2024.09.2 CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o CMakeFiles/Fingerprints.dir/MACCS.cpp.o CMakeFiles/Fingerprints.dir/MHFP.cpp.o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1 ../../../lib/libRDKitFingerprints.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +[ 40%] Built target Fingerprints make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake "--color=" @@ -4449,8 +4397,18 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 40%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFingerprintGenerator_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -MF CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o.d -o CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp -[ 40%] Linking CXX executable ForceFieldsCatch -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldsCatch.dir/link.txt --verbose=1 +[ 40%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -MF CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o.d -o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp +[ 40%] Linking CXX shared library ../../../lib/libRDKitMolHash.so +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolHash.dir/link.txt --verbose=1 +/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp: In function 'void RDKit::MMFF::Tools::addStretchBend(const RDKit::ROMol&, RDKit::MMFF::MMFFMolProperties*, ForceFields::ForceField*)': +/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp:419:68: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 419 | MMFF::Utils::calcStbnForceConstants(&mmffStbnParams); + | ^ +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolHash.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolHash.so.1 -o ../../../lib/libRDKitMolHash.so.1.2024.09.2 CMakeFiles/MolHash.dir/hashfunctions.cpp.o CMakeFiles/MolHash.dir/normalize.cpp.o ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolHash.so.1.2024.09.2 ../../../lib/libRDKitMolHash.so.1 ../../../lib/libRDKitMolHash.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +[ 40%] Built target MolHash make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/DependInfo.cmake "--color=" @@ -4459,78 +4417,26 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 41%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMHFPFingerprint_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -MF CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o.d -o CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/ForceFieldsCatch.dir/link.d CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o -o ForceFieldsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../lib/libRDKitForceField.so.1.2024.09.2 ../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 41%] Built target ForceFieldsCatch -[ 41%] Linking CXX shared library ../../lib/libRDKitDistGeometry.so -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeometry.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/DistGeometry.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeometry.so.1 -o ../../lib/libRDKitDistGeometry.so.1.2024.09.2 CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o CMakeFiles/DistGeometry.dir/DistViolationContribs.cpp.o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../lib/libRDKitForceField.so.1.2024.09.2 ../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDistGeometry.so.1.2024.09.2 ../../lib/libRDKitDistGeometry.so.1 ../../lib/libRDKitDistGeometry.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 41%] Built target DistGeometry -make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/DependInfo.cmake "--color=" -make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/DistGeom /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/DistGeom /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/DistGeom/CMakeFiles/testDistGeom.dir/DependInfo.cmake "--color=" -make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/DistGeom/Wrap /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/DistGeom/Wrap 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-fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o -MF CMakeFiles/DistGeom.dir/DistGeom.cpp.o.d -o CMakeFiles/DistGeom.dir/DistGeom.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/DistGeom/Wrap/DistGeom.cpp -[ 41%] Linking CXX executable forceFieldHelpersCatch -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/forceFieldHelpersCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/forceFieldHelpersCatch.dir/link.d CMakeFiles/forceFieldHelpersCatch.dir/catch_tests.cpp.o -o 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Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong 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../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 41%] Building CXX object Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS 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../../../../rdkit/Chem/rdDepictor.so +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDepictor.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdDepictor.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDepictor.so CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o ../../../../lib/libRDKitDepictor.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 41%] Built target rdMolHash -[ 41%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/DistGeomHelpers/EmbedderUtils.cpp +[ 41%] Built target rdDepictor [ 41%] Linking CXX shared module ../../../rdkit/Chem/rdinchi.so cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/External/INCHI-API/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdinchi.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdinchi.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdinchi.so CMakeFiles/rdinchi.dir/pyInchi.cpp.o ../../../lib/libRDKitRDInchiLib.so.1.2024.09.2 ../../../lib/libRDKitRDBoost.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libinchi.so ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 41%] Built target rdinchi -[ 41%] Linking CXX executable testDistGeom -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeom.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 41%] Built target testDistGeom -[ 41%] Linking CXX shared module ../../../rdkit/DistanceGeometry/DistGeom.so -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/DistGeom/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeom.dir/link.txt --verbose=1 -[ 41%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceFieldHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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'/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 41%] Built target rdForceFieldHelpers -[ 41%] Linking CXX shared module ../../../rdkit/ForceField/rdForceField.so -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ForceField/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceField.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdForceField.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ForceField/rdForceField.so CMakeFiles/rdForceField.dir/ForceField.cpp.o ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 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../../../lib/libRDKitChemTransforms.so cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ChemTransforms.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemTransforms.so.1 -o ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -4543,89 +4449,214 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 42%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o -[ 42%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o -[ 42%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -[ 42%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o +[ 41%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o +[ 41%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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-DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT 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CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/SmilesMolSupplier.cpp -[ 43%] Linking CXX shared module ../../../../rdkit/Chem/rdfiltercatalog.so -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfiltercatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdfiltercatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfiltercatalog.so CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../../lib/libRDKitCatalogs.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 42%] Built target rdMHFPFingerprint +make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/forceFieldHelpersCatch.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/forceFieldHelpersCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CMakeFiles/forceFieldHelpersCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 43%] Built target rdfiltercatalog -[ 43%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o -MF CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/SmilesWriter.cpp -[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o -MF CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o.d -o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/DistGeom/DistViolationContrib.cpp +[ 42%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFingerprintGenerator.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 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-I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -MF CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o.d -o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/DistGeom/ChiralViolationContrib.cpp +[ 43%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o -MF CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o.d -o CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/DistGeom/ChiralViolationContribs.cpp +[ 43%] Linking CXX executable forceFieldHelpersCatch +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/forceFieldHelpersCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/forceFieldHelpersCatch.dir/link.d 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cmake_link_script CMakeFiles/DistGeom.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/DistGeom.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/DistanceGeometry/DistGeom.so CMakeFiles/DistGeom.dir/DistGeom.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2024.09.2 ../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../lib/libRDKitForceField.so.1.2024.09.2 ../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +[ 44%] Built target DistGeom +[ 44%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/DistGeomHelpers/EmbedderUtils.cpp +[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.cpp +[ 45%] Linking CXX shared library ../../../lib/libRDKitDistGeomHelpers.so +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeomHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/DistGeomHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeomHelpers.so.1 -o ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.2 CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitDistGeometry.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitForceField.so.1.2024.09.2 ../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.2 ../../../lib/libRDKitDistGeomHelpers.so.1 ../../../lib/libRDKitDistGeomHelpers.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +[ 45%] Built target DistGeomHelpers [ 46%] Linking CXX shared library ../../../lib/libRDKitFileParsers.so cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/FileParsers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/FileParsers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFileParsers.so.1 -o ../../../lib/libRDKitFileParsers.so.1.2024.09.2 CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o CMakeFiles/FileParsers.dir/MolFileParser.cpp.o CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SDWriter.cpp.o CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o CMakeFiles/FileParsers.dir/TDTWriter.cpp.o CMakeFiles/FileParsers.dir/TplFileParser.cpp.o CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o CMakeFiles/FileParsers.dir/PDBParser.cpp.o CMakeFiles/FileParsers.dir/PDBWriter.cpp.o CMakeFiles/FileParsers.dir/CMLWriter.cpp.o CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o CMakeFiles/FileParsers.dir/MaeWriter.cpp.o CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o CMakeFiles/FileParsers.dir/SVGParser.cpp.o CMakeFiles/FileParsers.dir/PNGParser.cpp.o CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -4634,118 +4665,118 @@ [ 46%] Built target FileParsers make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/External/CoordGen 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/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTest1.dir/DependInfo.cmake "--color=" -make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol 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'/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/DependInfo.cmake "--color=" make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build -[ 46%] Building CXX object External/CoordGen/CMakeFiles/testCoordGen.dir/test.cpp.o -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/External/CoordGen && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT External/CoordGen/CMakeFiles/testCoordGen.dir/test.cpp.o -MF CMakeFiles/testCoordGen.dir/test.cpp.o.d -o CMakeFiles/testCoordGen.dir/test.cpp.o -c /build/reproducible-path/rdkit-202409.2/External/CoordGen/test.cpp +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol 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/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/DependInfo.cmake "--color=" +make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/build +make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +[ 46%] Building CXX object Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ForceField/UFF && /usr/bin/c++ 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -MF CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o.d -o CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/UFF/testUFFForceField.cpp +[ 47%] Building CXX object External/CoordGen/CMakeFiles/testCoordGen.dir/test.cpp.o +cd 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-I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT External/CoordGen/CMakeFiles/testCoordGen.dir/test.cpp.o -MF CMakeFiles/testCoordGen.dir/test.cpp.o.d -o CMakeFiles/testCoordGen.dir/test.cpp.o -c /build/reproducible-path/rdkit-202409.2/External/CoordGen/test.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -MF CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o.d -o CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/testMMFFForceField.cpp +[ 47%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -MF CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o.d -o CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/molopstest.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && 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'/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +[ 49%] Building CXX object Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -MF CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o.d -o CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/resMolSupplierTest.cpp -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -MF CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o.d -o CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/testMolBundle.cpp [ 49%] Building CXX object Code/GraphMol/CMakeFiles/testSGroup.dir/testSGroup.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD 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/build/reproducible-path/rdkit-202409.2/Code/GraphMol/testSGroup.cpp -[ 49%] Linking CXX executable resMolSupplierTest -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/resMolSupplierTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/resMolSupplierTest.dir/link.d CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -o resMolSupplierTest ../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so 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/usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 49%] Linking CXX executable resMolSupplierTest +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/resMolSupplierTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/resMolSupplierTest.dir/link.d CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -o resMolSupplierTest ../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 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-DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -MF CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o.d -o CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/catch_graphmol.cpp -[ 49%] Linking CXX executable hanoiTest -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/hanoiTest.dir/link.txt --verbose=1 -[ 49%] Linking CXX executable graphmoltestPicklerGlobalSetting -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPicklerGlobalSetting.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now 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49%] Linking CXX executable testUFFForceField +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ForceField/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceField.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testUFFForceField.dir/link.d CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -o testUFFForceField ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitForceField.so.1.2024.09.2 ../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 49%] Built target 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o -MF CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o.d -o CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/catch_organometallics.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection 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../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 49%] Linking CXX executable graphmoltestPicklerGlobalSetting +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPicklerGlobalSetting.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now 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make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 49%] Built target graphmoltestPicklerGlobalSetting +[ 49%] Built target hanoiTest make -f Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/DependInfo.cmake "--color=" @@ -4780,11 +4813,9 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 49%] Building CXX object Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -MF CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o.d -o CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/catch_sgroups.cpp -[ 49%] Linking CXX executable testUFFForceField -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ForceField/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceField.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing 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../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmoltestPicklerGlobalSetting.dir/link.d CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -o graphmoltestPicklerGlobalSetting ../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitAlignment.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 49%] Built target testUFFForceField +[ 49%] Built target graphmoltestPicklerGlobalSetting make -f Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/DependInfo.cmake "--color=" @@ -4819,13 +4850,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 49%] Building CXX object Code/GraphMol/CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o -MF CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o.d -o CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/catch_canon.cpp -[ 49%] Linking CXX executable testSGroup -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSGroup.dir/link.txt --verbose=1 [ 49%] Linking CXX executable graphmolOrganometallicsCatch cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolOrganometallicsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolOrganometallicsCatch.dir/link.d CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o -o graphmolOrganometallicsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitAlignment.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 49%] Built target testSGroup +[ 49%] Built target graphmolOrganometallicsCatch make -f Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/DependInfo.cmake "--color=" @@ -4834,9 +4863,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 49%] Building CXX object Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/catch_pickles.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD 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/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/DependInfo.cmake "--color=" @@ -4845,11 +4876,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 49%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/test.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK 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/usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 -ldl /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 +[ 49%] Linking CXX executable testSGroup +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSGroup.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSGroup.dir/link.d CMakeFiles/testSGroup.dir/testSGroup.cpp.o -o testSGroup ../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitAlignment.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 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/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Reaction.cpp -[ 49%] Linking CXX executable graphmolSGroupCatch -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolSGroupCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolSGroupCatch.dir/link.d CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -o graphmolSGroupCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitAlignment.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 49%] Linking CXX executable graphmolTest1 +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolTest1.dir/link.d CMakeFiles/graphmolTest1.dir/test1.cpp.o -o graphmolTest1 ../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../lib/libRDKitForceField.so.1.2024.09.2 ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 -ldl /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 49%] Built target graphmolSGroupCatch +[ 49%] Built target graphmolTest1 make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/DependInfo.cmake "--color=" @@ -4871,11 +4902,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 49%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/catch_tests.cpp -[ 49%] Linking CXX executable testMMFFForceField -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ForceField/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceField.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMMFFForceField.dir/link.d CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -o testMMFFForceField ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitDistGeometry.so.1.2024.09.2 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../lib/libRDKitForceField.so.1.2024.09.2 ../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 49%] Linking CXX executable graphmolSGroupCatch +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolSGroupCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolSGroupCatch.dir/link.d CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -o graphmolSGroupCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitAlignment.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 49%] Built target testMMFFForceField +[ 49%] Built target graphmolSGroupCatch make -f Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/DependInfo.cmake "--color=" @@ -4899,30 +4930,32 @@ cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DIN_COORDGEN -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/testDepictor.cpp.o -MF CMakeFiles/testDepictor.dir/testDepictor.cpp.o.d -o CMakeFiles/testDepictor.dir/testDepictor.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Depictor/testDepictor.cpp [ 50%] Linking CXX executable graphmoltestPickler cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPickler.dir/link.txt --verbose=1 -[ 50%] Linking CXX executable canonTestsCatch -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/canonTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmoltestPickler.dir/link.d CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -o graphmoltestPickler ../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitAlignment.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/canonTestsCatch.dir/link.d CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o -o canonTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitAlignment.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 50%] Built target graphmoltestPickler make -f Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/build.make Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +make -f Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/build.make Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +[ 50%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DIN_COORDGEN -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT 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Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/build.make Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/catch_tests.cpp.o -MF CMakeFiles/depictorCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/depictorCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Depictor/catch_tests.cpp +[ 50%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/MDLParser.cpp [ 50%] Linking CXX executable graphmoltestChirality cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestChirality.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmoltestChirality.dir/link.d CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -o graphmoltestChirality ../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitAlignment.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so @@ -4949,8 +4982,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.cpp.o -MF CMakeFiles/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.cpp.o.d -o CMakeFiles/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/testSquiggleDoubleBonds.cpp -[ 50%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -MF CMakeFiles/ChemReactions.dir/MDLParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/MDLParser.cpp [ 50%] Linking CXX executable nontetrahedralCatch cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/nontetrahedralCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nontetrahedralCatch.dir/link.d CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o -o nontetrahedralCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so @@ -4977,6 +5008,8 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -MF CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o.d -o CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/testGeneralFileReader.cpp +[ 50%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -MF CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/DaylightParser.cpp [ 50%] Linking CXX executable testAtropisomers cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAtropisomers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testAtropisomers.dir/link.d CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o -o testAtropisomers ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so @@ -4990,8 +5023,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -MF CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o.d -o CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/testMultithreadedMolSupplier.cpp -[ 50%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -MF CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/DaylightParser.cpp [ 50%] Linking CXX executable testDepictor cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDepictor.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testDepictor.dir/link.d CMakeFiles/testDepictor.dir/testDepictor.cpp.o -o testDepictor ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so @@ -5005,10 +5036,10 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -MF CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o.d -o CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/testMolWriter.cpp -[ 50%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/ReactionPickler.cpp [ 50%] Linking CXX executable testGeneralFileReader cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGeneralFileReader.dir/link.txt --verbose=1 +[ 50%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/ReactionPickler.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testGeneralFileReader.dir/link.d CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -o testGeneralFileReader ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitRDStreams.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 50%] Built target testGeneralFileReader @@ -5033,11 +5064,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -MF CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o.d -o CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/testMol2ToMol.cpp -[ 50%] Linking CXX executable testMol2ToMol -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMol2ToMol.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMol2ToMol.dir/link.d CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -o testMol2ToMol ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 50%] Linking CXX executable testTplParser +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTplParser.dir/link.txt --verbose=1 +[ 50%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/ReactionWriter.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testTplParser.dir/link.d CMakeFiles/testTplParser.dir/testTpls.cpp.o -o testTplParser ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 50%] Built target testMol2ToMol +[ 50%] Built target testTplParser make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/DependInfo.cmake "--color=" @@ -5046,11 +5079,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o -MF CMakeFiles/testSequence.dir/testSequence.cpp.o.d -o CMakeFiles/testSequence.dir/testSequence.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/testSequence.cpp -[ 50%] Linking CXX executable testMolSupplier -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolSupplier.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolSupplier.dir/link.d CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -o testMolSupplier ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitRDStreams.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 +[ 50%] Linking CXX executable testMol2ToMol +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMol2ToMol.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMol2ToMol.dir/link.d CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -o testMol2ToMol ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 50%] Built target testMolSupplier +[ 50%] Built target testMol2ToMol make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/DependInfo.cmake "--color=" @@ -5059,13 +5092,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -MF CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o.d -o CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/testExtendedStereoParsing.cpp -[ 50%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/ReactionWriter.cpp -[ 50%] Linking CXX executable testTplParser -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTplParser.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testTplParser.dir/link.d CMakeFiles/testTplParser.dir/testTpls.cpp.o -o testTplParser ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 50%] Linking CXX executable graphmolTestsCatch +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolTestsCatch.dir/link.d CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -o graphmolTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitAlignment.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 50%] Built target testTplParser +[ 50%] Built target graphmolTestsCatch make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/DependInfo.cmake "--color=" @@ -5074,21 +5105,21 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -MF CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o.d -o CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/file_parsers_catch.cpp -[ 50%] Linking CXX executable graphmolTestsCatch -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolTestsCatch.dir/link.d CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -o graphmolTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 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--verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/depictorCatch.dir/link.d CMakeFiles/depictorCatch.dir/catch_tests.cpp.o -o depictorCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 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'/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o +[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED 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../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 51%] Built target testMolWriter +[ 50%] Built target smiTest1 make -f Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/build.make 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-I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -MF CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o.d -o CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/molfile_stereo_catch.cpp -[ 51%] Linking CXX executable smiTest1 -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/smiTest1.dir/link.d CMakeFiles/smiTest1.dir/test.cpp.o -o smiTest1 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 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cmake_link_script CMakeFiles/testMolSupplier.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/smiTestCatch.dir/link.d CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -o smiTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 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/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/depictorCatch.dir/link.d CMakeFiles/depictorCatch.dir/catch_tests.cpp.o -o depictorCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o +[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -MF CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o.d -o CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/connectTheDots_catch.cpp -[ 51%] Built target depictorCatch +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolSupplier.dir/link.d CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -o testMolSupplier ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitRDStreams.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +[ 50%] Built target testMolSupplier make -f Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/depend make[4]: Entering directory 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Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o +[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o -MF CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o.d -o CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/v2_suppliers_catch.cpp -[ 51%] Linking CXX executable chiralityTestsCatch -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/chiralityTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/chiralityTestsCatch.dir/link.d CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o -o chiralityTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitCIPLabeler.so.1.2024.09.2 ../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitAlignment.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 50%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/ReactionDepict.cpp +[ 51%] Linking CXX executable testMolWriter +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolWriter.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolWriter.dir/link.d CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -o testMolWriter ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 51%] Built target chiralityTestsCatch +[ 51%] Built target testMolWriter make -f Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/DependInfo.cmake "--color=" @@ -5165,25 +5198,25 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o -MF CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o.d -o CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/v2_file_parsers_catch.cpp -[ 51%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/ReactionDepict.cpp -[ 52%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/ReactionFingerprints.cpp -[ 52%] Linking CXX executable v2MolSuppliers -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/v2MolSuppliers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/v2MolSuppliers.dir/link.d CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o -o v2MolSuppliers ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 51%] Linking CXX executable testExtendedStereoParsing +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testExtendedStereoParsing.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testExtendedStereoParsing.dir/link.d CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -o testExtendedStereoParsing ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 52%] Built target v2MolSuppliers +[ 51%] Built target testExtendedStereoParsing make -f Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o +[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o -MF CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o.d -o CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FileParsers/multithreaded_supplier_catch.cpp +[ 52%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/ReactionFingerprints.cpp [ 52%] Linking CXX executable XYZFileParserCatchTest cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/XYZFileParserCatchTest.dir/link.txt --verbose=1 +[ 52%] Linking CXX executable connectTheDotsTest +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/connectTheDotsTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/XYZFileParserCatchTest.dir/link.d CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -o XYZFileParserCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 52%] Built target XYZFileParserCatchTest @@ -5195,8 +5228,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o -MF CMakeFiles/testSubstructMatch.dir/test1.cpp.o.d -o CMakeFiles/testSubstructMatch.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/test1.cpp -[ 53%] Linking CXX executable connectTheDotsTest -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/connectTheDotsTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/connectTheDotsTest.dir/link.d CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -o connectTheDotsTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 53%] Built target connectTheDotsTest @@ -5208,13 +5239,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/catch_tests.cpp -[ 53%] Linking CXX executable smiTestCatch -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTestCatch.dir/link.txt --verbose=1 [ 53%] Linking CXX executable v2FileParsersCatchTest -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/smiTestCatch.dir/link.d CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -o smiTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/v2FileParsersCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/v2FileParsersCatchTest.dir/link.d CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o -o v2FileParsersCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 53%] Built target smiTestCatch +[ 53%] Built target v2FileParsersCatchTest make -f Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/DependInfo.cmake "--color=" @@ -5223,9 +5252,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -MF CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o.d -o CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemTransforms/testChemTransforms.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/v2FileParsersCatchTest.dir/link.d CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o -o v2FileParsersCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 53%] Linking CXX executable v2MolSuppliers +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/v2MolSuppliers.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/v2MolSuppliers.dir/link.d CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o -o v2MolSuppliers ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 53%] Built target v2FileParsersCatchTest +[ 53%] Built target v2MolSuppliers make -f Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/DependInfo.cmake "--color=" @@ -5247,6 +5278,8 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -MF CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o.d -o CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/filtercatalogtest.cpp +[ 53%] Linking CXX executable multithreadedSupplierCatchTest +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/multithreadedSupplierCatchTest.dir/link.txt --verbose=1 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/test1.cpp: In function 'void testMostSubstitutedCoreMatch()': /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/test1.cpp:1903:41: warning: possibly dangling reference to a temporary [-Wdangling-reference] 1903 | std::make_pair(phenyl.get(), 3u)}) { @@ -5278,12 +5311,6 @@ /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Substruct/test1.cpp:1903:23: note: the temporary was destroyed at the end of the full expression 'std::make_pair(phenyl.std::unique_ptr::get(), 3)' 1903 | std::make_pair(phenyl.get(), 3u)}) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -[ 53%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/ReactionUtils.cpp -[ 53%] Linking CXX executable multithreadedSupplierCatchTest -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/multithreadedSupplierCatchTest.dir/link.txt --verbose=1 -[ 53%] Linking CXX executable graphmolMolOpsTest -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMolOpsTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/multithreadedSupplierCatchTest.dir/link.d CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o -o multithreadedSupplierCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 53%] Built target multithreadedSupplierCatchTest @@ -5295,9 +5322,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o -MF CMakeFiles/testFragCatalog.dir/test1.cpp.o.d -o CMakeFiles/testFragCatalog.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog/test1.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolMolOpsTest.dir/link.d CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -o graphmolMolOpsTest ../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitAlignment.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 53%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/ReactionUtils.cpp +[ 53%] Linking CXX executable cdxmlParserCatchTest +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/cdxmlParserCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/cdxmlParserCatchTest.dir/link.d CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -o cdxmlParserCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 53%] Built target graphmolMolOpsTest +[ 53%] Built target cdxmlParserCatchTest make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog/Wrap /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/DependInfo.cmake "--color=" @@ -5306,11 +5337,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o -MF CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog/Wrap/rdfragcatalog.cpp -[ 53%] Linking CXX executable cdxmlParserCatchTest -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/cdxmlParserCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/cdxmlParserCatchTest.dir/link.d CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -o cdxmlParserCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 53%] Linking CXX executable graphmolMolOpsTest +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMolOpsTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolMolOpsTest.dir/link.d CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -o graphmolMolOpsTest ../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../lib/libRDKitAlignment.so.1.2024.09.2 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 53%] Built target cdxmlParserCatchTest +[ 53%] Built target graphmolMolOpsTest make -f Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/DependInfo.cmake "--color=" @@ -5332,10 +5363,10 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/test1.cpp.o -MF CMakeFiles/testFingerprints.dir/test1.cpp.o.d -o CMakeFiles/testFingerprints.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/test1.cpp -[ 53%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -MF CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/MoleculeParser.cpp [ 53%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog/Wrap/FragCatalog.cpp +[ 53%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -MF CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/MoleculeParser.cpp [ 53%] Linking CXX executable filterCatalogTest cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/filterCatalogTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/filterCatalogTest.dir/link.d CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -o filterCatalogTest ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so @@ -5349,11 +5380,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -MF CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o.d -o CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/testMHFPFingerprint.cpp -[ 53%] Linking CXX executable fileParsersTest1 -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fileParsersTest1.dir/link.d CMakeFiles/fileParsersTest1.dir/test1.cpp.o -o fileParsersTest1 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 53%] Linking CXX executable testFragCatalog +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFragCatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testFragCatalog.dir/link.d CMakeFiles/testFragCatalog.dir/test1.cpp.o -o testFragCatalog ../../../lib/libRDKitFragCatalog.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 53%] Built target fileParsersTest1 +[ 53%] Built target testFragCatalog make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/DependInfo.cmake "--color=" @@ -5364,13 +5395,11 @@ cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -MF CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o.d -o CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp [ 54%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o -MF CMakeFiles/Descriptors.dir/BCUT.cpp.o.d -o CMakeFiles/Descriptors.dir/BCUT.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/BCUT.cpp -[ 54%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/ReactionRunner.cpp -[ 54%] Linking CXX executable testFragCatalog -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFragCatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testFragCatalog.dir/link.d CMakeFiles/testFragCatalog.dir/test1.cpp.o -o testFragCatalog ../../../lib/libRDKitFragCatalog.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 54%] Linking CXX executable substructTestCatch +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/substructTestCatch.dir/link.d CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -o substructTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 54%] Built target testFragCatalog +[ 54%] Built target substructTestCatch make -f Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/DependInfo.cmake "--color=" @@ -5379,11 +5408,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 54%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/catch_tests.cpp -[ 54%] Linking CXX executable substructTestCatch -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/substructTestCatch.dir/link.d CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -o substructTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 54%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/ReactionRunner.cpp +[ 54%] Linking CXX executable testMHFPFingerprint +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMHFPFingerprint.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMHFPFingerprint.dir/link.d CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -o testMHFPFingerprint ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 54%] Built target substructTestCatch +[ 54%] Built target testMHFPFingerprint make -f Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/DependInfo.cmake "--color=" @@ -5392,11 +5423,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 55%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o -MF CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o.d -o CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/fpgen_catch_tests.cpp -[ 55%] Linking CXX executable testMHFPFingerprint -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMHFPFingerprint.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMHFPFingerprint.dir/link.d CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -o testMHFPFingerprint ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 55%] Linking CXX executable testSubstructMatch +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubstructMatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSubstructMatch.dir/link.d CMakeFiles/testSubstructMatch.dir/test1.cpp.o -o testSubstructMatch ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 55%] Built target testMHFPFingerprint +[ 55%] Built target testSubstructMatch make -f Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/DependInfo.cmake "--color=" @@ -5405,11 +5436,17 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 55%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/test1.cpp.o -MF CMakeFiles/testMolTransforms.dir/test1.cpp.o.d -o CMakeFiles/testMolTransforms.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolTransforms/test1.cpp -[ 55%] Linking CXX executable testSubstructMatch -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubstructMatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSubstructMatch.dir/link.d CMakeFiles/testSubstructMatch.dir/test1.cpp.o -o testSubstructMatch ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 55%] Linking CXX executable testChemTransforms +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemTransforms.dir/link.txt --verbose=1 +/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/BCUT.cpp: In function 'std::pair RDKit::Descriptors::{anonymous}::BCUT2D(std::unique_ptr >&, const std::vector&)': +/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/BCUT.cpp:70:71: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 70 | const std::vector &atom_props) { + | ^ +[ 55%] Linking CXX executable chemTransformsTestCatch +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/chemTransformsTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testChemTransforms.dir/link.d CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -o testChemTransforms ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 55%] Built target testSubstructMatch +[ 55%] Built target testChemTransforms make -f Code/GraphMol/MolTransforms/CMakeFiles/molTransformsTestCatch.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/molTransformsTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/molTransformsTestCatch.dir/DependInfo.cmake "--color=" @@ -5418,14 +5455,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 55%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/molTransformsTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolTransforms/CMakeFiles/molTransformsTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/molTransformsTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/molTransformsTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolTransforms/catch_tests.cpp -/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/BCUT.cpp: In function 'std::pair RDKit::Descriptors::{anonymous}::BCUT2D(std::unique_ptr >&, const std::vector&)': -/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/BCUT.cpp:70:71: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 70 | const std::vector &atom_props) { - | ^ -[ 55%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog/Wrap/FragCatParams.cpp -[ 55%] Linking CXX executable chemTransformsTestCatch -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/chemTransformsTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/chemTransformsTestCatch.dir/link.d CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -o chemTransformsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 55%] Built target chemTransformsTestCatch @@ -5437,11 +5466,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 55%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -MF CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o.d -o CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFHelpers.cpp -[ 55%] Linking CXX executable testChemTransforms -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemTransforms.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testChemTransforms.dir/link.d CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -o testChemTransforms ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 55%] Linking CXX executable fileParsersTest1 +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fileParsersTest1.dir/link.d CMakeFiles/fileParsersTest1.dir/test1.cpp.o -o fileParsersTest1 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 55%] Built target testChemTransforms +[ 55%] Built target fileParsersTest1 make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/DependInfo.cmake "--color=" @@ -5450,21 +5479,23 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 55%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -MF CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o.d -o CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/MMFF/testMultiThread.cpp -[ 55%] Linking CXX executable fpGenTestCatch -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpGenTestCatch.dir/link.txt --verbose=1 -[ 56%] Linking CXX executable molTransformsTestCatch -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/molTransformsTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fpGenTestCatch.dir/link.d CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o -o fpGenTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 55%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog/Wrap/FragCatParams.cpp +[ 55%] Linking CXX executable testMolTransforms +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolTransforms.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolTransforms.dir/link.d CMakeFiles/testMolTransforms.dir/test1.cpp.o -o testMolTransforms ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 56%] Built target fpGenTestCatch +[ 55%] Built target testMolTransforms make -f Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/UFF /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 56%] Building CXX object Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o +[ 55%] Building CXX object Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -MF CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o.d -o CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp +[ 56%] Linking CXX executable molTransformsTestCatch +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/molTransformsTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molTransformsTestCatch.dir/link.d CMakeFiles/molTransformsTestCatch.dir/catch_tests.cpp.o -o molTransformsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 56%] Built target molTransformsTestCatch @@ -5476,11 +5507,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 56%] Building CXX object Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -MF CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o.d -o CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalFF.cpp -[ 56%] Linking CXX executable testMolTransforms -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolTransforms.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolTransforms.dir/link.d CMakeFiles/testMolTransforms.dir/test1.cpp.o -o testMolTransforms ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 56%] Linking CXX executable fpGenTestCatch +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpGenTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fpGenTestCatch.dir/link.d CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o -o fpGenTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 56%] Built target testMolTransforms +[ 56%] Built target fpGenTestCatch make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/DependInfo.cmake "--color=" @@ -5489,11 +5520,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 56%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -MF CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o.d -o CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp -[ 56%] Linking CXX executable fpTestCatch -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fpTestCatch.dir/link.d CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -o fpTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 56%] Linking CXX executable testMMFFForceFieldHelpersMultiThread +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/link.d CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -o testMMFFForceFieldHelpersMultiThread ../../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.2 ../../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../../lib/libRDKitDistGeometry.so.1.2024.09.2 ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../../lib/libRDKitForceField.so.1.2024.09.2 ../../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 56%] Built target fpTestCatch +[ 56%] Built target testMMFFForceFieldHelpersMultiThread make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/DependInfo.cmake "--color=" @@ -5502,15 +5533,15 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 56%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -MF CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/DistGeomHelpers/catch_tests.cpp -[ 56%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -MF CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o.d -o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/PreprocessRxn.cpp [ 56%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog/Wrap/FragCatGenerator.cpp -[ 56%] Linking CXX executable fileParsersCatchTest -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 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../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 56%] Linking CXX executable fpTestCatch +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpTestCatch.dir/link.txt --verbose=1 +[ 56%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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'/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 56%] Built target fileParsersCatchTest +[ 56%] Built target fpTestCatch make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/DistGeomHelpers/Wrap /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/DependInfo.cmake "--color=" @@ -5519,11 +5550,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 57%] Building CXX object Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_MAX_ARITY=32 -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDistGeom_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -MF CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o.d -o CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp -[ 57%] Linking CXX executable testMMFFForceFieldHelpersMultiThread -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/link.d CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -o testMMFFForceFieldHelpersMultiThread ../../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.2 ../../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../../lib/libRDKitDistGeometry.so.1.2024.09.2 ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../../lib/libRDKitForceField.so.1.2024.09.2 ../../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 57%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/MolDescriptors.cpp +[ 57%] Linking CXX executable fileParsersCatchTest +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fileParsersCatchTest.dir/link.d CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -o fileParsersCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 57%] Built target testMMFFForceFieldHelpersMultiThread +[ 57%] Built target fileParsersCatchTest make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/DependInfo.cmake "--color=" @@ -5532,11 +5565,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 57%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -MF CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o.d -o CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign/testMolAlign.cpp -[ 57%] Linking CXX executable testFingerprintGenerators -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprintGenerators.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testFingerprintGenerators.dir/link.d CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -o testFingerprintGenerators ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 57%] Linking CXX executable testMMFFForceFieldHelpers +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMMFFForceFieldHelpers.dir/link.d CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -o testMMFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.2 ../../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../../lib/libRDKitDistGeometry.so.1.2024.09.2 ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../../lib/libRDKitForceField.so.1.2024.09.2 ../../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 57%] Built target testFingerprintGenerators +[ 57%] Built target testMMFFForceFieldHelpers make -f Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/DependInfo.cmake "--color=" @@ -5560,23 +5593,23 @@ cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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CMakeFiles/testFeatures.dir/testFeatures.cpp.o.d -o CMakeFiles/testFeatures.dir/testFeatures.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp [ 57%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -MF CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o.d -o CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/SanitizeRxn.cpp -[ 57%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/MolDescriptors.cpp -[ 57%] Linking CXX executable testMMFFForceFieldHelpers -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMMFFForceFieldHelpers.dir/link.d CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -o testMMFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.2 ../../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../../lib/libRDKitDistGeometry.so.1.2024.09.2 ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../../lib/libRDKitForceField.so.1.2024.09.2 ../../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 57%] Linking CXX executable testFingerprintGenerators +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprintGenerators.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testFingerprintGenerators.dir/link.d CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -o testFingerprintGenerators ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 57%] Built target testMMFFForceFieldHelpers +[ 57%] Built target testFingerprintGenerators make -f Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' make -f Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 57%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog/Wrap/FragFPGenerator.cpp [ 57%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -MF CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o.d -o CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ShapeHelpers/testShapeHelpers.cpp +[ 57%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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-fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog/Wrap/FragFPGenerator.cpp [ 57%] Linking CXX executable testFingerprints cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprints.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testFingerprints.dir/link.d CMakeFiles/testFingerprints.dir/test1.cpp.o -o testFingerprints ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so @@ -5590,39 +5623,39 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 57%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o -MF CMakeFiles/testMolCatalog.dir/test1.cpp.o.d -o CMakeFiles/testMolCatalog.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolCatalog/test1.cpp -[ 57%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o -MF CMakeFiles/Descriptors.dir/MolSurf.cpp.o.d -o CMakeFiles/Descriptors.dir/MolSurf.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/MolSurf.cpp -[ 57%] Linking CXX executable testMolAlign -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolAlign.dir/link.txt --verbose=1 -[ 57%] Linking CXX executable molAlignCatchTest -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/molAlignCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now 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../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 58%] Linking CXX executable testShapeHelpers +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testShapeHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testShapeHelpers.dir/link.d CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -o testShapeHelpers ../../../lib/libRDKitShapeHelpers.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 57%] Built target testMolAlign +[ 58%] Built target testShapeHelpers make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/DependInfo.cmake "--color=" 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/FMCS.cpp.o -MF CMakeFiles/FMCS.dir/FMCS.cpp.o.d -o CMakeFiles/FMCS.dir/FMCS.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/FMCS.cpp +[ 59%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PNGParser.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -MF CMakeFiles/ChemReactions.dir/PNGParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/PNGParser.cpp +[ 59%] Linking CXX executable molAlignCatchTest +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/molAlignCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molAlignCatchTest.dir/link.d CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -o molAlignCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 58%] Built target molAlignCatchTest +[ 59%] Built target molAlignCatchTest make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolHash 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-DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMMPA_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MMPA_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/MMPA.cpp.o -MF CMakeFiles/MMPA.dir/MMPA.cpp.o.d -o CMakeFiles/MMPA.dir/MMPA.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MMPA/MMPA.cpp -[ 60%] Linking CXX shared module ../../../../rdkit/Chem/rdDistGeom.so -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDistGeom.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdDistGeom.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDistGeom.so 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rdDistGeom +[ 60%] Built target rdfragcatalog make -f Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/build.make Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/DependInfo.cmake "--color=" +[ 60%] Linking CXX executable testUFFForceFieldHelpers +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/cmake -E cmake_link_script 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-Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testUFFForceFieldHelpers.dir/link.d CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -o testUFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.2 ../../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../../lib/libRDKitDistGeometry.so.1.2024.09.2 ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../../lib/libRDKitForceField.so.1.2024.09.2 ../../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 60%] Built target testUFFForceFieldHelpers @@ -5659,21 +5690,23 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 60%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -MF CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o.d -o CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Trajectory/trajectoryTest.cpp -[ 60%] Linking CXX shared module ../../../../rdkit/Chem/rdfragcatalog.so -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfragcatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdfragcatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfragcatalog.so CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o ../../../../lib/libRDKitFragCatalog.so.1.2024.09.2 ../../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 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-DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o -MF CMakeFiles/Descriptors.dir/Lipinski.cpp.o.d -o CMakeFiles/Descriptors.dir/Lipinski.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/Lipinski.cpp +[ 60%] Linking CXX executable testFeatures +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFeatures.dir/link.txt --verbose=1 +[ 61%] Linking CXX executable testMolCatalog +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolCatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testFeatures.dir/link.d CMakeFiles/testFeatures.dir/testFeatures.cpp.o -o testFeatures ../../../lib/libRDKitMolChemicalFeatures.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 60%] Built target rdfragcatalog +[ 61%] Built target testFeatures make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 60%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o +[ 61%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/build/reproducible-path/rdkit-202409.2/External/rapidjson-1.1.0/include -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -MF CMakeFiles/molInterchangeTest1.dir/test1.cpp.o.d -o CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolInterchange/test1.cpp -[ 61%] Linking CXX executable testMolCatalog -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolCatalog.dir/link.d CMakeFiles/testMolCatalog.dir/test1.cpp.o -o testMolCatalog ../../../lib/libRDKitMolCatalog.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 61%] Built target testMolCatalog @@ -5682,14 +5715,14 @@ cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/build -[ 61%] Linking CXX executable testFeatures -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFeatures.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 61%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/build/reproducible-path/rdkit-202409.2/External/rapidjson-1.1.0/include -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -MF CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o.d -o CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolInterchange/molinterchange_catch.cpp -/usr/bin/c++ -g -O2 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../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 61%] Linking CXX shared module ../../../../rdkit/Chem/rdDistGeom.so +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDistGeom.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdDistGeom.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDistGeom.so CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o ../../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.2 ../../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitDistGeometry.so.1.2024.09.2 ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../../lib/libRDKitForceField.so.1.2024.09.2 ../../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 61%] Built target testFeatures +[ 61%] Built target rdDistGeom make -f Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/DependInfo.cmake "--color=" @@ -5698,8 +5731,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 61%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o cd 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../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so @@ -5734,10 +5765,10 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 63%] Linking CXX executable trajectoryTest -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryTest.dir/link.txt --verbose=1 [ 63%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -MF CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o.d -o CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MMPA/MMPA_UnitTest.cpp +[ 63%] Linking CXX executable trajectoryTest +cd 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../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitForceField.so.1.2024.09.2 ../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 63%] Built target trajectoryTest @@ -5749,84 +5780,84 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 63%] Building CXX object Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMMPA_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -MF CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o.d -o CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MMPA/Wrap/rdMMPA.cpp -[ 63%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD 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Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o -MF CMakeFiles/Descriptors.dir/MQN.cpp.o.d -o CMakeFiles/Descriptors.dir/MQN.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/MQN.cpp -[ 63%] Linking CXX executable molInterchangeCatchTest -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeCatchTest.dir/link.txt --verbose=1 -[ 64%] Linking CXX shared library ../../../lib/libRDKitMolProcessing.so +[ 64%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK 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CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp +[ 65%] Linking CXX shared library ../../../lib/libRDKitMolProcessing.so cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolProcessing.dir/link.txt --verbose=1 -[ 64%] Linking CXX executable testAbbreviations -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAbbreviations.dir/link.txt --verbose=1 -[ 64%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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/usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +[ 65%] Linking CXX executable molInterchangeCatchTest +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolProcessing.dir/link.d -Wl,-z,relro -Wl,-z,now -shared 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../../../lib/libRDKitRDGeneral.so.1.2024.09.2 -ldl /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolProcessing.so.1.2024.09.2 ../../../lib/libRDKitMolProcessing.so.1 ../../../lib/libRDKitMolProcessing.so -[ 64%] Built target molInterchangeCatchTest -[ 64%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD 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../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so -[ 64%] Built target MolProcessing make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +[ 65%] Built target MolProcessing make -f Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/build.make Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolProcessing 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../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' make[4]: Leaving directory 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o -MF CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o.d -o CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/AUTOCORR2D.cpp +[ 65%] Built target molInterchangeCatchTest +make -f 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/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/MQN.cpp +[ 65%] Linking CXX executable molInterchangeTest1 +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molInterchangeTest1.dir/link.d CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -o molInterchangeTest1 ../../../lib/libRDKitMolInterchange.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 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Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o -MF CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o.d -o CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MarvinParse/MarvinDefs.cpp make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/RDF.cpp.o -MF CMakeFiles/Descriptors.dir/RDF.cpp.o.d -o CMakeFiles/Descriptors.dir/RDF.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/RDF.cpp +[ 67%] Linking CXX shared library ../../../lib/libRDKitFMCS.so +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FMCS 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/WHIM.cpp.o -MF CMakeFiles/Descriptors.dir/WHIM.cpp.o.d -o CMakeFiles/Descriptors.dir/WHIM.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/WHIM.cpp +[ 68%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/CoulombMat.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/CoulombMat.cpp.o -MF CMakeFiles/Descriptors.dir/CoulombMat.cpp.o.d -o CMakeFiles/Descriptors.dir/CoulombMat.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/CoulombMat.cpp make -f 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../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +[ 68%] Built target testReactionFingerprints make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 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-DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Pipeline.cpp.o -MF CMakeFiles/MolStandardize.dir/Pipeline.cpp.o.d -o CMakeFiles/MolStandardize.dir/Pipeline.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/Pipeline.cpp -[ 68%] Linking CXX shared library ../../../lib/libRDKitFMCS.so -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCS.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/FMCS.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFMCS.so.1 -o ../../../lib/libRDKitFMCS.so.1.2024.09.2 CMakeFiles/FMCS.dir/FMCS.cpp.o CMakeFiles/FMCS.dir/Seed.cpp.o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o 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/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFMCS.so.1.2024.09.2 ../../../lib/libRDKitFMCS.so.1 ../../../lib/libRDKitFMCS.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 68%] Built target FMCS make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/MolDraw2D.cpp -[ 69%] Linking CXX shared library ../../../lib/libRDKitRascalMCES.so -cd 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/usr/include/c++/14/bits/stl_algobase.h:64, from /usr/include/c++/14/bits/stl_tree.h:63, from /usr/include/c++/14/map:62, @@ -5968,11 +5996,25 @@ /usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1132 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ -[ 69%] Linking CXX executable testReactionFingerprints -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReactionFingerprints.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -MF CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o.d -o CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/MolStandardize.cpp +[ 70%] Linking CXX shared library ../../../lib/libRDKitMarvinParser.so +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/MarvinParser.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MarvinParser.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMarvinParser.so.1 -o ../../../lib/libRDKitMarvinParser.so.1.2024.09.2 CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMarvinParser.so.1.2024.09.2 ../../../lib/libRDKitMarvinParser.so.1 ../../../lib/libRDKitMarvinParser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 69%] Built target testEnumeration +[ 70%] Built target MarvinParser make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Test /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu 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/build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Test/testFMCS.cpp -[ 69%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp -[ 69%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o -MF CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o.d -o CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/AtomSymbol.cpp -[ 69%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawAnnotation.cpp -[ 69%] Linking CXX executable FMCStest -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Test && /usr/bin/cmake -E 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Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMolMCH.cpp +[ 70%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.cpp +[ 70%] Building CXX object 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object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawTextNotFT.cpp +[ 70%] Linking CXX shared module ../../../../rdkit/Chem/rdFMCS.so +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFMCS.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. 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../../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 69%] Built target FMCStest +[ 70%] Built target rdFMCS make -f Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/build.make Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/depend make[4]: Entering 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Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o +[ 70%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. 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Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o -MF CMakeFiles/MolStandardize.dir/Metal.cpp.o.d -o CMakeFiles/MolStandardize.dir/Metal.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/Metal.cpp -[ 69%] Linking CXX shared library ../../../lib/libRDKitMarvinParser.so -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/MarvinParser.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MarvinParser.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMarvinParser.so.1 -o ../../../lib/libRDKitMarvinParser.so.1.2024.09.2 CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMarvinParser.so.1.2024.09.2 ../../../lib/libRDKitMarvinParser.so.1 ../../../lib/libRDKitMarvinParser.so +In file included from /usr/include/c++/14/vector:62, + from /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:15: +In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = int; _Up = int; bool _IsMove = false]', + inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, + inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, + inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31, + inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7, + inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27, + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*; _Tp = int]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:1022:38, + inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1488:19, + inlined from 'void RDKit::MolDraw2D_detail::DrawMolMCHLasso::extractAtomColourLists(std::vector&, std::vector >&, std::vector >&) const' at /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:115:32: +/usr/include/c++/14/bits/stl_algobase.h:452:30: warning: 'void* __builtin_memmove(void*, const void*, long unsigned int)' writing between 5 and 9223372036854775804 bytes into a region of size 0 overflows the destination [-Wstringop-overflow=] + 452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/aarch64-linux-gnu/c++/14/bits/c++allocator.h:33, + from /usr/include/c++/14/bits/allocator.h:46, + from /usr/include/c++/14/vector:63: +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = int]', + inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = int]' at /usr/include/c++/14/bits/alloc_traits.h:509:28, + inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:380:33, + inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:1013:40, + inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1488:19, + inlined from 'void RDKit::MolDraw2D_detail::DrawMolMCHLasso::extractAtomColourLists(std::vector&, std::vector >&, std::vector >&) const' at /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:115:32: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: at offset [-9223372036854775808, -1] into destination object of size [4, 9223372036854775804] allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +[ 70%] Linking CXX executable FMCStest +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Test && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCStest.dir/link.txt --verbose=1 +In file included from /usr/include/c++/14/bits/stl_algobase.h:64, + from /usr/include/c++/14/string:51, + from /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawText.h:19, + from /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawText.cpp:13: +/usr/include/c++/14/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': +/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawText.cpp:165:47: required from here + 165 | tl = mol_draw.getAtomCoords(std::make_pair(tl.x, tl.y)); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1132 | make_pair(_T1&& __x, _T2&& __y) + | ^~~~~~~~~ +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/FMCStest.dir/link.d CMakeFiles/FMCStest.dir/testFMCS.cpp.o -o FMCStest ../../../../lib/libRDKitFMCS.so.1.2024.09.2 ../../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 69%] Built target MarvinParser +[ 70%] Built target FMCStest make -f Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/build.make Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' make -f Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/build.make Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 69%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o +[ 70%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -MF CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o.d -o CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/mces_cluster_catch.cpp -[ 69%] Linking CXX shared library ../../../lib/libRDKitDescriptors.so +[ 70%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawTextSVG.cpp +[ 70%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/MolDraw2DJS.cpp +[ 70%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.cpp -[ 70%] Linking CXX executable testRascalCluster +[ 71%] Linking CXX executable testRascalCluster cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRascalCluster.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRascalCluster.dir/link.d CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -o testRascalCluster ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRascalMCES.so.1.2024.09.2 /usr/lib/libCatch2.a 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-I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/rdmolops.cpp.o -MF CMakeFiles/rdmolops.dir/rdmolops.cpp.o.d -o CMakeFiles/rdmolops.dir/rdmolops.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/rdmolops.cpp -[ 70%] Linking CXX executable testRascalMCES +[ 71%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 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/usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 70%] Built target testRascalMCES +[ 71%] Linking CXX shared library ../../../lib/libRDKitMolDraw2D.so +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolDraw2D.dir/link.txt --verbose=1 +[ 71%] Built target testRascalMCES make -f Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap 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-DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o -MF CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o.d -o CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/rdmolfiles.cpp -In file included from /usr/include/c++/14/vector:62, - from /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:15: -In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = int; _Up = int; bool _IsMove = false]', - inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, - inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, - inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31, - inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7, - inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27, - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*; _Tp = int]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:1022:38, - inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1488:19, - inlined from 'void RDKit::MolDraw2D_detail::DrawMolMCHLasso::extractAtomColourLists(std::vector&, std::vector >&, std::vector >&) const' at /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:115:32: -/usr/include/c++/14/bits/stl_algobase.h:452:30: warning: 'void* __builtin_memmove(void*, const void*, long unsigned int)' writing between 5 and 9223372036854775804 bytes into a region of size 0 overflows the destination [-Wstringop-overflow=] - 452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/aarch64-linux-gnu/c++/14/bits/c++allocator.h:33, - from /usr/include/c++/14/bits/allocator.h:46, - from /usr/include/c++/14/vector:63: -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = int]', - inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = int]' at /usr/include/c++/14/bits/alloc_traits.h:509:28, - inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:380:33, - inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:1013:40, - inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1488:19, - inlined from 'void RDKit::MolDraw2D_detail::DrawMolMCHLasso::extractAtomColourLists(std::vector&, std::vector >&, std::vector >&) const' at /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:115:32: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: at offset [-9223372036854775808, -1] into destination object of size [4, 9223372036854775804] allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -[ 70%] Linking CXX executable rxnTestCatch -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/rxnTestCatch.dir/link.txt --verbose=1 -[ 70%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o -MF CMakeFiles/MolStandardize.dir/Charge.cpp.o.d -o CMakeFiles/MolStandardize.dir/Charge.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/Charge.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard 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../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolDraw2D.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolDraw2D.so.1 -o ../../../lib/libRDKitMolDraw2D.so.1.2024.09.2 CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o CMakeFiles/MolDraw2D.dir/DrawText.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o ../../../lib/libRDKitChemReactions.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libfreetype.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcairo.so +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolDraw2D.so.1.2024.09.2 ../../../lib/libRDKitMolDraw2D.so.1 ../../../lib/libRDKitMolDraw2D.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 70%] Built target rxnTestCatch +[ 71%] Built target MolDraw2D make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 70%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o +[ 71%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -MF CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o.d -o CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SmilesParse/cxsmiles_test.cpp -[ 70%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -MF 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-I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o -MF CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/CIPMol.cpp -[ 71%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawText.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawText.cpp -[ 71%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o -MF CMakeFiles/rdmolops.dir/MolOps.cpp.o.d -o CMakeFiles/rdmolops.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/MolOps.cpp -[ 71%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawTextNotFT.cpp -In file included from /usr/include/c++/14/bits/stl_algobase.h:64, - from /usr/include/c++/14/string:51, - from /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawText.h:19, - from /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawText.cpp:13: -/usr/include/c++/14/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': -/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawText.cpp:165:47: required from here - 165 | tl = mol_draw.getAtomCoords(std::make_pair(tl.x, tl.y)); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1132 | make_pair(_T1&& __x, _T2&& __y) - | ^~~~~~~~~ -[ 71%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o -MF CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/CIPLabeler.cpp -[ 71%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -MF CMakeFiles/MolStandardize.dir/Tautomer.cpp.o.d -o CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/Tautomer.cpp -[ 71%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawTextSVG.cpp -[ 71%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/MolDraw2DJS.cpp -[ 71%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/DrawTextJS.cpp -[ 72%] 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-I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/MolDraw2DCairo.cpp -[ 72%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp -[ 75%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION 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-I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/testMORSE.cpp.o -MF CMakeFiles/testMORSE.dir/testMORSE.cpp.o.d -o CMakeFiles/testMORSE.dir/testMORSE.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/testMORSE.cpp -[ 80%] Linking CXX shared library ../../../lib/libRDKitMolStandardize.so -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/test3D.cpp.o -MF CMakeFiles/test3D.dir/test3D.cpp.o.d -o CMakeFiles/test3D.dir/test3D.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/test3D.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdmolops.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdmolops.so CMakeFiles/rdmolops.dir/rdmolops.cpp.o CMakeFiles/rdmolops.dir/MolOps.cpp.o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitRDBoost.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' In file included from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, @@ -6506,15 +6446,6 @@ /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 80%] Built target rdmolops -make -f Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/build.make 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object Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/testWHIM.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/testWHIM.cpp.o -MF CMakeFiles/testWHIM.dir/testWHIM.cpp.o.d -o CMakeFiles/testWHIM.dir/testWHIM.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/testWHIM.cpp In copy constructor 'boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]', inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]' at /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:25: /usr/include/boost/smart_ptr/shared_ptr.hpp:459:66: warning: '*(const boost::shared_ptr*)((char*)& + offsetof(boost::python::extract >,boost::python::extract >::.boost::python::converter::extract_rvalue >::m_data.boost::python::converter::rvalue_from_python_data >::.boost::python::converter::rvalue_from_python_storage >::storage)).boost::shared_ptr::px' may be used uninitialized [-Wmaybe-uninitialized] @@ -6534,39 +6465,119 @@ /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 81%] Linking CXX executable testPBF +[ 75%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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/build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp +[ 76%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp +[ 76%] Linking CXX executable testEEM +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testEEM.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp +[ 77%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o +cd 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Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -MF CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o.d -o CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/rxn_test1.cpp +[ 83%] Linking CXX executable testCoulombMat +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoulombMat.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testCoulombMat.dir/link.d CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o -o testCoulombMat ../../../lib/libRDKitDescriptors.so.1.2024.09.2 ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.2 ../../../lib/libRDKitPartialCharges.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitDistGeometry.so.1.2024.09.2 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitForceField.so.1.2024.09.2 ../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../lib/libRDKitTrajectory.so.1.2024.09.2 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Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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+/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp:444:61: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 444 | python::list atomprops) { + | ^ In file included from /usr/include/c++/14/bits/stl_algobase.h:64, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3906, @@ -6702,27 +6701,140 @@ /usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1132 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ -[ 85%] Linking CXX executable descriptorsTestCatch +[ 83%] Linking CXX executable descriptorsTestCatch cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/descriptorsTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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-Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/MaeWriter.cpp +[ 83%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.cpp +[ 83%] Linking CXX executable moldraw2DRxnTest1 +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DRxnTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 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-[ 85%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o +[ 83%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDeprotect_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o -MF CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o.d -o CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Deprotect/Wrap/rdDeprotect.cpp -[ 85%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so +[ 83%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/O3AAlign.dir/link.txt --verbose=1 -[ 85%] Linking CXX executable moldraw2DRxnTest1 -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DRxnTest1.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/O3AAlign.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitO3AAlign.so.1 -o ../../../lib/libRDKitO3AAlign.so.1.2024.09.2 CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o 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-Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -MF CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o.d -o CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/enumerator_catch.cpp +[ 83%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong 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-o ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 CMakeFiles/MolStandardize.dir/Pipeline.cpp.o CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o CMakeFiles/MolStandardize.dir/Metal.cpp.o CMakeFiles/MolStandardize.dir/Normalize.cpp.o CMakeFiles/MolStandardize.dir/Validate.cpp.o CMakeFiles/MolStandardize.dir/Charge.cpp.o CMakeFiles/MolStandardize.dir/Tautomer.cpp.o CMakeFiles/MolStandardize.dir/Fragment.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitMolStandardize.so.1 ../../../lib/libRDKitMolStandardize.so +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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'/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +[ 85%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o +[ 85%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include 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/build/reproducible-path/rdkit-202409.2/Code/GraphMol/TautomerQuery/TautomerQuery.cpp +[ 85%] Linking CXX executable testMolEnumerator +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolEnumerator.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolEnumerator.dir/link.d CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -o testMolEnumerator ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +[ 85%] Built target testMolEnumerator make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/DependInfo.cmake "--color=" @@ -6731,11 +6843,28 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 85%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/test1.cpp.o -MF CMakeFiles/molStandardizeTest.dir/test1.cpp.o.d -o CMakeFiles/molStandardizeTest.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/test1.cpp -[ 85%] Linking CXX executable deprotectTest -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_link_script CMakeFiles/deprotectTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/moldraw2DRxnTest1.dir/link.d CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -o moldraw2DRxnTest1 ../../../lib/libRDKitMolDraw2D.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcairo.so /usr/lib/aarch64-linux-gnu/libfreetype.so +In file included from /usr/include/c++/14/bits/stl_algobase.h:64, + from /usr/include/c++/14/string:51, + from /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/Invariant.h:17, + from /build/reproducible-path/rdkit-202409.2/Code/Numerics/Matrix.h:14, + from /build/reproducible-path/rdkit-202409.2/Code/Numerics/SquareMatrix.h:14, + from /build/reproducible-path/rdkit-202409.2/Code/Geometry/Transform3D.h:16, + from /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign/AlignMolecules.h:14, + from /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign/testO3AAlign.cpp:11: +/usr/include/c++/14/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': +/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign/testO3AAlign.cpp:643:37: required from here + 643 | oscores.push_back(std::make_pair(rmsd, score)); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1132 | make_pair(_T1&& __x, _T2&& __y) + | ^~~~~~~~~ +[ 85%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/TDTWriter.cpp +[ 85%] Linking CXX executable moldraw2DTest1 +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/moldraw2DTest1.dir/link.d CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -o moldraw2DTest1 ../../../lib/libRDKitMolDraw2D.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libmaeparser.so 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'/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 85%] Built target moldraw2DRxnTest1 +[ 85%] Built target moldraw2DTest1 make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/DependInfo.cmake "--color=" @@ -6744,9 +6873,11 @@ make[4]: Entering directory 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../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcairo.so /usr/lib/aarch64-linux-gnu/libfreetype.so /usr/lib/aarch64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 85%] Built target deprotectTest +[ 85%] Built target rdMolDraw2D make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/DependInfo.cmake "--color=" @@ -6755,358 +6886,256 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 85%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/testValidate.cpp.o cd 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/TDTMolSupplier.cpp -[ 85%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o -cd 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../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../lib/libRDKitTautomerQuery.so.1 ../../../lib/libRDKitTautomerQuery.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 85%] Built target molValidateTest +[ 87%] Built target TautomerQuery make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 85%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o +[ 87%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -MF CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o.d -o CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/testTautomer.cpp -[ 85%] Linking CXX executable molStandardizeTest -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 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../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 87%] Linking CXX shared module ../../../../rdkit/Chem/rdMolAlign.so +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolAlign.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -MF CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o.d -o CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/test2.cpp -[ 85%] Linking CXX shared module ../../../../rdkit/Chem/rdDeprotect.so 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../../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 87%] Linking CXX executable molNormalizeTest +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molNormalizeTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molNormalizeTest.dir/link.d CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -o molNormalizeTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 85%] Built target rdDeprotect +[ 87%] Built target molNormalizeTest make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 85%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/testFragment.cpp.o +[ 87%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/testFragment.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -MF CMakeFiles/rdchem.dir/MonomerInfo.cpp.o.d -o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/MonomerInfo.cpp -[ 85%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizePipelineTest.dir/testPipeline.cpp.o -MF CMakeFiles/molStandardizePipelineTest.dir/testPipeline.cpp.o.d -o CMakeFiles/molStandardizePipelineTest.dir/testPipeline.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/testPipeline.cpp -[ 86%] Building CXX object 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Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -MF CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o.d -o CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolEnumerator/Wrap/rdMolEnumerator.cpp -[ 87%] Linking CXX shared module ../../../../rdkit/Chem/Draw/rdMolDraw2D.so -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDraw2D.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 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Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 87%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_TAUTOMERQUERY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DTautomerQuery_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o -MF CMakeFiles/rdchem.dir/MolBundle.cpp.o.d -o CMakeFiles/rdchem.dir/MolBundle.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/MolBundle.cpp -[ 88%] Linking CXX shared library ../../../lib/libRDKitScaffoldNetwork.so -cd 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CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -o molTautomerTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolAlign_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -MF CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o.d -o CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp -[ 88%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/StereoGroup.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/StereoGroup.cpp.o -MF CMakeFiles/rdchem.dir/StereoGroup.cpp.o.d -o CMakeFiles/rdchem.dir/StereoGroup.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/StereoGroup.cpp -[ 89%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/TautomerQuery.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/TautomerQuery.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTautomerQuery.so.1 -o ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../lib/libRDKitTautomerQuery.so.1 ../../../lib/libRDKitTautomerQuery.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 89%] Built target TautomerQuery -make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -make -f 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -MF CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o.d -o CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ScaffoldNetwork/catch_tests.cpp -[ 90%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Validate.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/Wrap/Validate.cpp -[ 90%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/SDWriter.cpp -In file included from /usr/include/c++/14/bits/stl_algobase.h:64, - from /usr/include/c++/14/string:51, - from /build/reproducible-path/rdkit-202409.2/Code/RDGeneral/Invariant.h:17, - from /build/reproducible-path/rdkit-202409.2/Code/Numerics/Matrix.h:14, - from /build/reproducible-path/rdkit-202409.2/Code/Numerics/SquareMatrix.h:14, - from /build/reproducible-path/rdkit-202409.2/Code/Geometry/Transform3D.h:16, - from /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign/AlignMolecules.h:14, - from /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign/testO3AAlign.cpp:11: -/usr/include/c++/14/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': -/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign/testO3AAlign.cpp:643:37: required from here - 643 | oscores.push_back(std::make_pair(rmsd, score)); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1132 | make_pair(_T1&& __x, _T2&& __y) - | ^~~~~~~~~ -[ 90%] Linking CXX shared module ../../../../rdkit/Chem/rdMolEnumerator.so -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolEnumerator.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 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../../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 90%] Built target rdMolEnumerator -make -f Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/DependInfo.cmake "--color=" +cd 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/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdScaffoldNetwork_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -MF CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o.d -o CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ScaffoldNetwork/Wrap/rdScaffoldNetwork.cpp -[ 91%] Linking CXX executable molStandardizePipelineTest -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizePipelineTest.dir/link.txt --verbose=1 -[ 91%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -MF CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o.d -o CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/SubstanceGroup.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molStandardizePipelineTest.dir/link.d CMakeFiles/molStandardizePipelineTest.dir/testPipeline.cpp.o -o molStandardizePipelineTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 91%] Built target molStandardizePipelineTest -make -f Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -cd 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CXX object Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o -MF CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o.d -o CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.cpp +[ 89%] Linking CXX executable molChargeTest +cd 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'/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 91%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupDecomp.cpp -[ 91%] Linking CXX shared module ../../../../rdkit/Chem/rdMolAlign.so -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolAlign.dir/link.txt --verbose=1 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../../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitForceField.so.1.2024.09.2 ../../../../lib/libRDKitOptimizer.so.1.2024.09.2 ../../../../lib/libRDKitTrajectory.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 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Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGeneralizedSubstruct_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GENERALIZEDSUBSTRUCT_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupDecomp.cpp +[ 92%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. 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/usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -MF CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o.d -o CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ScaffoldNetwork/Wrap/rdScaffoldNetwork.cpp +[ 94%] Linking CXX executable molTautomerTest +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molTautomerTest.dir/link.txt --verbose=1 +[ 94%] Building CXX object 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../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 93%] Built target testScaffoldNetwork -[ 93%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o +[ 94%] Built target molTautomerTest +[ 94%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK 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Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Metal.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/Wrap/Metal.cpp +[ 94%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION 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module ../../../../rdkit/Chem/rdTautomerQuery.so cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdTautomerQuery.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdScaffoldNetwork.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o ../../../../lib/libRDKitScaffoldNetwork.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 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../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdTautomerQuery.dir/link.d 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target rdTautomerQuery [ 94%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code 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molStandardizePipelineTest +[ 94%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupData.cpp +[ 94%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o -MF CMakeFiles/rdchem.dir/RingInfo.cpp.o.d -o CMakeFiles/rdchem.dir/RingInfo.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/RingInfo.cpp +[ 94%] Linking CXX executable molStandardizeCatchTest +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now 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Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 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-I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupUtils.cpp [ 94%] Linking CXX shared library ../../../lib/libRDKitGeneralizedSubstruct.so 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -MF CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o.d -o CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp -[ 94%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_BUILD 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/usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 95%] Built target rdchem -[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_op.c.o +[ 96%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_op.c.o -MF CMakeFiles/rdkit.dir/bfp_op.c.o.d -o CMakeFiles/rdkit.dir/bfp_op.c.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/bfp_op.c -[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/cache.c.o +[ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/cache.c.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && 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CMakeFiles/rdkit.dir/mol_op.c.o -c /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/mol_op.c -[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_gist.c.o +[ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_gist.c.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.2\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS 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Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gist.c.o +[ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gist.c.o cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.2\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/build/reproducible-path/rdkit-202409.2/Code -I/usr/include/postgresql 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-Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupFingerprintScore.cpp -[ 97%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/RGroupGa.cpp -[ 97%] Linking CXX shared module ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolStandardize.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolStandardize.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o CMakeFiles/rdMolStandardize.dir/Charge.cpp.o CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o CMakeFiles/rdMolStandardize.dir/Metal.cpp.o CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o ../../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 97%] Built target rdMolStandardize [ 97%] Linking CXX shared module ../../../../rdkit/Chem/rdGeneralizedSubstruct.so cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeneralizedSubstruct.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdGeneralizedSubstruct.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdGeneralizedSubstruct.so CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [ 97%] Built target rdGeneralizedSubstruct -[ 97%] Linking CXX shared library librdkit.so -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/sql /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/PgSQL/rdkit/sql -cd 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../../../lib/libRDKitMolDraw2D.so.1.2024.09.2 ../../../lib/libRDKitMolHash.so.1.2024.09.2 ../../../lib/libRDKitFMCS.so.1.2024.09.2 ../../../lib/libRDKitDescriptors.so.1.2024.09.2 ../../../lib/libRDKitPartialCharges.so.1.2024.09.2 ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcairo.so /usr/lib/aarch64-linux-gnu/libfreetype.so ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 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'/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 97%] Built target generalizedSubstructCatch -[ 97%] Linking CXX shared library ../../../lib/libRDKitSubstructLibrary.so -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructLibrary.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SubstructLibrary.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubstructLibrary.so.1 -o ../../../lib/libRDKitSubstructLibrary.so.1.2024.09.2 CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.2 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructLibrary.so.1.2024.09.2 ../../../lib/libRDKitSubstructLibrary.so.1 ../../../lib/libRDKitSubstructLibrary.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 97%] Built target SubstructLibrary -make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make 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../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructLibrary.so.1.2024.09.2 ../../../lib/libRDKitSubstructLibrary.so.1 ../../../lib/libRDKitSubstructLibrary.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[ 99%] Built target gaExample -[ 99%] Linking CXX executable substructLibraryCatchTest -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryCatchTest.dir/link.txt --verbose=1 +[ 97%] Built target SubstructLibrary +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.2 /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build +[ 97%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -MF CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o.d -o CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +[ 98%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.2/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstructLibrary/catch_tests.cpp +[ 99%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp +[ 99%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202409.2/External -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202409.2/Code -I/build/reproducible-path/rdkit-202409.2/External/boost-numeric-bindings -isystem /usr/include/python3.12 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -c /build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp +[ 99%] Linking CXX shared library librdkit.so +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/sql /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/PgSQL/rdkit/sql +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/data /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/PgSQL/rdkit/data +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/expected /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/PgSQL/rdkit/expected +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdkit.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/rdkit.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,librdkit.so -o librdkit.so CMakeFiles/rdkit.dir/adapter.cpp.o CMakeFiles/rdkit.dir/bfp_op.c.o CMakeFiles/rdkit.dir/cache.c.o CMakeFiles/rdkit.dir/guc.c.o CMakeFiles/rdkit.dir/low_gist.c.o CMakeFiles/rdkit.dir/mol_op.c.o CMakeFiles/rdkit.dir/rdkit_gist.c.o CMakeFiles/rdkit.dir/bfp_gist.c.o CMakeFiles/rdkit.dir/bfp_gin.c.o CMakeFiles/rdkit.dir/bitstring.c.o CMakeFiles/rdkit.dir/rdkit_io.c.o CMakeFiles/rdkit.dir/rxn_op.c.o CMakeFiles/rdkit.dir/sfp_op.c.o -L/build/reproducible-path/rdkit-202409.2/Code/PgSQL/rdkit/lib /usr/lib/aarch64-linux-gnu/libpq.so ../../../lib/libRDKitRDInchiLib.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libinchi.so ../../../lib/libRDKitMolInterchange.so.1.2024.09.2 ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.2 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../lib/libRDKitMolDraw2D.so.1.2024.09.2 ../../../lib/libRDKitMolHash.so.1.2024.09.2 ../../../lib/libRDKitFMCS.so.1.2024.09.2 ../../../lib/libRDKitDescriptors.so.1.2024.09.2 ../../../lib/libRDKitPartialCharges.so.1.2024.09.2 ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcairo.so /usr/lib/aarch64-linux-gnu/libfreetype.so ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 -ldl /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +[ 99%] Built target rdkit +[ 99%] Linking CXX shared module ../../../rdkit/Chem/rdchem.so +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdchem.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdchem.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdchem.so CMakeFiles/rdchem.dir/rdchem.cpp.o CMakeFiles/rdchem.dir/Table.cpp.o CMakeFiles/rdchem.dir/Atom.cpp.o CMakeFiles/rdchem.dir/Bond.cpp.o CMakeFiles/rdchem.dir/Mol.cpp.o CMakeFiles/rdchem.dir/Conformer.cpp.o CMakeFiles/rdchem.dir/RingInfo.cpp.o CMakeFiles/rdchem.dir/EditableMol.cpp.o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o CMakeFiles/rdchem.dir/MolBundle.cpp.o CMakeFiles/rdchem.dir/StereoGroup.cpp.o CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o CMakeFiles/rdchem.dir/Chirality.cpp.o ../../../lib/libRDKitMarvinParser.so.1.2024.09.2 ../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +[ 99%] Built target rdchem [100%] Linking CXX executable testRGroupDecompInternals cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecompInternals.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/substructLibraryCatchTest.dir/link.d CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -o substructLibraryCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.2 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[100%] Built target substructLibraryCatchTest /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRGroupDecompInternals.dir/link.d CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -o testRGroupDecompInternals ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.2 ../../../lib/libRDKitFMCS.so.1.2024.09.2 ../../../lib/libRDKitga.so.1.2024.09.2 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [100%] Built target testRGroupDecompInternals -[100%] Linking CXX executable substructLibraryTest -cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/substructLibraryTest.dir/link.d CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -o substructLibraryTest ../../../lib/libRDKitSubstructLibrary.so.1.2024.09.2 ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.2 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[100%] Linking CXX executable gaExample +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/gaExample.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gaExample.dir/link.d CMakeFiles/gaExample.dir/GaExample.cpp.o -o gaExample ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 ../../../lib/libRDKitFMCS.so.1.2024.09.2 ../../../lib/libRDKitga.so.1.2024.09.2 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' -[100%] Built target substructLibraryTest +[100%] Built target gaExample [100%] Linking CXX shared module ../../../../rdkit/Chem/rdRGroupDecomposition.so cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRGroupDecomposition.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdRGroupDecomposition.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRGroupDecomposition.so CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o ../../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.2 ../../../../lib/libRDKitRDBoost.so.1.2024.09.2 ../../../../lib/libRDKitFMCS.so.1.2024.09.2 ../../../../lib/libRDKitga.so.1.2024.09.2 ../../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../../lib/libRDKitCatalogs.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_numpy312.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' [100%] Built target rdRGroupDecomposition +[100%] Linking CXX executable substructLibraryTest +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/substructLibraryTest.dir/link.d CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -o substructLibraryTest ../../../lib/libRDKitSubstructLibrary.so.1.2024.09.2 ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.2 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +[100%] Built target substructLibraryTest +[100%] Linking CXX executable substructLibraryCatchTest +cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/substructLibraryCatchTest.dir/link.d CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -o substructLibraryCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.2 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu' +[100%] Built target substructLibraryCatchTest [100%] Linking CXX executable rgroupCatchTests cd /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/rgroupCatchTests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/rgroupCatchTests.dir/link.d CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -o rgroupCatchTests ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.2 /usr/lib/libCatch2.a ../../../lib/libRDKitFMCS.so.1.2024.09.2 ../../../lib/libRDKitga.so.1.2024.09.2 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.2 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.2 ../../../lib/libRDKitMolStandardize.so.1.2024.09.2 ../../../lib/libRDKitChemReactions.so.1.2024.09.2 ../../../lib/libRDKitFingerprints.so.1.2024.09.2 ../../../lib/libRDKitFileParsers.so.1.2024.09.2 ../../../lib/libRDKitChemTransforms.so.1.2024.09.2 ../../../lib/libRDKitDepictor.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.2 ../../../lib/libRDKitMolTransforms.so.1.2024.09.2 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.2 ../../../lib/libRDKitAlignment.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.2 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.2 ../../../lib/libRDKitGenericGroups.so.1.2024.09.2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.2 ../../../lib/libRDKitSubgraphs.so.1.2024.09.2 ../../../lib/libRDKitGraphMol.so.1.2024.09.2 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.2 ../../../lib/libRDKitDataStructs.so.1.2024.09.2 ../../../lib/libRDKitCatalogs.so.1.2024.09.2 ../../../lib/libRDKitRDGeneral.so.1.2024.09.2 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -12875,7 +12906,7 @@ GettingStartedInC++ resolving references... -WARNING: Could not fetch remote image: https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC [HTTPSConnectionPool(host='img.shields.io', port=443): Max retries exceeded with url: /badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC (Caused by NameResolutionError(": Failed to resolve 'img.shields.io' ([Errno -3] Temporary failure in name resolution)"))] +WARNING: Could not fetch remote image: https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC [HTTPSConnectionPool(host='img.shields.io', port=443): Max retries exceeded with url: /badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC (Caused by NameResolutionError(": Failed to resolve 'img.shields.io' ([Errno -3] Temporary failure in name resolution)"))] processing RDKit.tex: done writing... done copying images... [ 1%] images/Cc1ccccc1.png @@ -15940,13 +15971,12 @@ 12: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/testBV.py" 12: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/DataStructs/Wrap 12: Test timeout computed to be: 1500 -3: [02:22:45] Testing Github940: property dictionaries leaking memory -3: [02:22:45] done +3: [23:09:28] Testing Github940: property dictionaries leaking memory +3: [23:09:29] done 3: Testing RDValue 3: Testing RDAny 3: dict set int vect 3: dict get int vect -3: static boost any:0.04699 s 4: -- running tests -- 4: min: -2147483648 -2147483648 4: min: 0 0 @@ -15959,48 +15989,38 @@ 4: == unsigned int 4: == bool 4: == std::string -5: [02:22:45] +5: [23:09:28] 5: ----------------------------------------- -5: [02:22:45] Finished: testPushAndPop() -5: [02:22:45] +5: [23:09:29] Finished: testPushAndPop() +5: [23:09:29] 5: ----------------------------------------- -5: [02:22:45] +5: [23:09:29] 5: ----------------------------------------- -6: Randomness seeded to: 833192205 -6: =============================================================================== -6: All tests passed (32 assertions in 2 test cases) -6: -7: [02:22:45] should not be silent -7: [02:22:45] should not be silent -7: Randomness seeded to: 567841421 -7: [02:22:45] should not be silent -7: [02:22:45] should not be silent -7: [02:22:45] should not be silent -7: [02:22:45] should not be silent -7: [02:22:45] should not be silent -7: [02:22:45] should not be silent -7: [02:22:45] should not be silent -7: [02:22:45] should not be silent -7: =============================================================================== -7: All tests passed (26 assertions in 3 test cases) -7: -8: [02:22:45] pass -8: [02:22:45] v3 4 -8: [02:22:45] v4 5 -8: [02:22:45] SPARSE ----------------------------------- -8: [02:22:45] Set 10: 0 -8: [02:22:45] Set 11: 0 -8: [02:22:45] Set 14: 0 -8: [02:22:45] Set 10: 1 -8: [02:22:45] Get 14: 1 -8: [02:22:45] Num: 20 -8: [02:22:45] NumOn: 3 -8: [02:22:45] NumOff: 17 +8: [23:09:29] pass +8: [23:09:29] v3 4 +8: [23:09:29] v4 5 +8: [23:09:29] SPARSE ----------------------------------- +8: [23:09:29] Set 10: 0 +8: [23:09:29] Set 11: 0 +8: [23:09:29] Set 14: 0 +8: [23:09:29] Set 10: 1 +8: [23:09:29] Get 14: 1 +8: [23:09:29] Num: 20 +8: [23:09:29] NumOn: 3 +8: [23:09:29] NumOff: 17 + 1/230 Test #4: testRDValue ............................ Passed 0.24 sec +test 13 + Start 13: pyDiscreteValueVect + +13: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/testDiscreteValueVect.py" +13: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/DataStructs/Wrap +13: Test timeout computed to be: 1500 +3: static boost any:0.047213 s 8: 10, 11, 14, -8: [02:22:45] t2[19]: 0 -8: [02:22:45] t2[14]: 1 -8: [02:22:45] t2[19]: 0 -8: [02:22:45] t2[14]: 0 +8: [23:09:29] t2[19]: 0 +8: [23:09:29] t2[14]: 1 +8: [23:09:29] t2[19]: 0 +8: [23:09:29] t2[14]: 0 8: t1: 10, 11, 14, 8: t2: 10, 11, 15, 17, 8: t1|t2: 10, 11, 14, 15, 17, @@ -16008,20 +16028,27 @@ 8: t1^t2: 14, 15, 17, 8: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19, 8: except -8: [02:22:45] Explicit ---------------------------------- -8: [02:22:45] Set 10: 0 -8: [02:22:45] Set 11: 0 -8: [02:22:45] Set 14: 0 -8: [02:22:45] Set 10: 1 -8: [02:22:45] Get 14: 1 -8: [02:22:45] Num: 20 -8: [02:22:45] NumOn: 3 -8: [02:22:45] NumOff: 17 +8: [23:09:29] Explicit ---------------------------------- +8: [23:09:29] Set 10: 0 +8: [23:09:29] Set 11: 0 +8: [23:09:29] Set 14: 0 +8: [23:09:29] Set 10: 1 +8: [23:09:29] Get 14: 1 +8: [23:09:29] Num: 20 +8: [23:09:29] NumOn: 3 +8: [23:09:29] NumOff: 17 + 2/230 Test #9: testFPB ................................ Passed 0.14 sec +test 14 + Start 14: pySparseIntVect + +14: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/testSparseIntVect.py" +14: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/DataStructs/Wrap +14: Test timeout computed to be: 1500 8: 10, 11, 14, -8: [02:22:45] t2[19]: 0 -8: [02:22:45] t2[14]: 1 -8: [02:22:45] t2[19]: 0 -8: [02:22:45] t2[14]: 0 +8: [23:09:29] t2[19]: 0 +8: [23:09:29] t2[14]: 1 +8: [23:09:29] t2[19]: 0 +8: [23:09:29] t2[14]: 0 8: t1: 10, 11, 14, 8: t2: 10, 11, 15, 17, 8: t1|t2: 10, 11, 14, 15, 17, @@ -16029,63 +16056,63 @@ 8: t1^t2: 14, 15, 17, 8: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19, 8: except -8: [02:22:45] Done -8: [02:22:45] Test DiscreteValue Vectors 1 ---------------------------- -8: [02:22:45] Expected failure: Value out of range -8: [02:22:45] Expected failure: Value out of range -8: [02:22:45] Expected failure: Value out of range -8: [02:22:45] Expected failure: Value out of range -8: [02:22:45] Expected failure: Value out of range -8: [02:22:45] Test DiscreteValue Vectors 2 ------------------------------ -8: [02:22:45] Test DiscreteValue Vectors 3 --------------------------- -8: [02:22:45] Test DiscreteValue Operations ----------------------------- -8: [02:22:45] Test DiscreteValue Operations 2 -------------------------- -8: [02:22:45] Test SparseIntVect ------------------------------------ -8: [02:22:45] Test SparseIntVect Serialization -------------------------- -8: [02:22:45] Test BitVect Serialization ------------------------------- -8: [02:22:45] Test BitVect to FPS ------------------------------- -8: [02:22:45] Test BitVect to binary string ------------------------------- -8: [02:22:45] Test Similarity Measures BitVect ------------------------------- -8: [02:22:45] Test Similarity Measures SparseBitVect ------------------------------- -8: [02:22:45] Test BitVect with all ones ------------------------------- -8: [02:22:45] Test Explicit BitVects: Concatenation Operation ------------------------------- -8: [02:22:45] Test bitmap operations ------------------------------- -8: [02:22:45] Test bitmaps as properties ------------------------------- -8: [02:22:45] Test #3944: SparseIntVect copy constructor and assignment operators not clearing existing data------------------------------- -11: Randomness seeded to: 1119119797 -11: =============================================================================== -11: All tests passed (3 assertions in 1 test case) -11: - 1/230 Test #4: testRDValue ............................ Passed 0.09 sec - 2/230 Test #6: dictTestsCatch ......................... Passed 0.08 sec - 3/230 Test #7: logTestsCatch .......................... Passed 0.07 sec - 4/230 Test #8: testDataStructs ........................ Passed 0.06 sec - 5/230 Test #9: testFPB ................................ Passed 0.05 sec - 6/230 Test #11: catchDataStructs ....................... Passed 0.02 sec -test 13 - Start 13: pyDiscreteValueVect - -13: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/testDiscreteValueVect.py" -13: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/DataStructs/Wrap -13: Test timeout computed to be: 1500 -test 14 - Start 14: pySparseIntVect - -14: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/testSparseIntVect.py" -14: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/DataStructs/Wrap -14: Test timeout computed to be: 1500 +8: [23:09:29] Done +8: [23:09:29] Test DiscreteValue Vectors 1 ---------------------------- +8: [23:09:29] Expected failure: Value out of range +8: [23:09:29] Expected failure: Value out of range +8: [23:09:29] Expected failure: Value out of range +8: [23:09:29] Expected failure: Value out of range +8: [23:09:29] Expected failure: Value out of range +8: [23:09:29] Test DiscreteValue Vectors 2 ------------------------------ +8: [23:09:29] Test DiscreteValue Vectors 3 --------------------------- +8: [23:09:29] Test DiscreteValue Operations ----------------------------- +8: [23:09:29] Test DiscreteValue Operations 2 -------------------------- +8: [23:09:29] Test SparseIntVect ------------------------------------ +8: [23:09:29] Test SparseIntVect Serialization -------------------------- +8: [23:09:29] Test BitVect Serialization ------------------------------- +8: [23:09:29] Test BitVect to FPS ------------------------------- +8: [23:09:29] Test BitVect to binary string ------------------------------- +8: [23:09:29] Test Similarity Measures BitVect ------------------------------- +8: [23:09:29] Test Similarity Measures SparseBitVect ------------------------------- +8: [23:09:29] Test BitVect with all ones ------------------------------- +8: [23:09:29] Test Explicit BitVects: Concatenation Operation ------------------------------- +8: [23:09:29] Test bitmap operations ------------------------------- +8: [23:09:29] Test bitmaps as properties ------------------------------- +8: [23:09:29] Test #3944: SparseIntVect copy constructor and assignment operators not clearing existing data------------------------------- + 3/230 Test #8: testDataStructs ........................ Passed 0.27 sec test 15 Start 15: pyFPB 15: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/DataStructs/Wrap/testFPB.py" 15: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/DataStructs/Wrap 15: Test timeout computed to be: 1500 +6: Randomness seeded to: 135133577 +6: =============================================================================== +6: All tests passed (32 assertions in 2 test cases) +6: +7: [23:09:29] should not be silent +7: [23:09:29] should not be silent +7: Randomness seeded to: 2143344838 +7: [23:09:29] should not be silent + 4/230 Test #6: dictTestsCatch ......................... Passed 0.36 sec test 16 Start 16: testTransforms 16: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/Geometry/testTransforms 16: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/Geometry 16: Test timeout computed to be: 1500 +7: [23:09:29] should not be silent +7: [23:09:29] should not be silent +7: [23:09:29] should not be silent +7: [23:09:29] should not be silent +7: [23:09:29] should not be silent +7: [23:09:29] should not be silent +7: [23:09:29] should not be silent +7: =============================================================================== +7: All tests passed (26 assertions in 3 test cases) +7: + 5/230 Test #7: logTestsCatch .......................... Passed 0.36 sec + 6/230 Test #10: testMultiFPB ........................... Passed 0.28 sec test 17 Start 17: testGrid @@ -16106,8 +16133,8 @@ 16: testPointOps2D 16: **************************************** 16: test12D -16: ref1: 2.1736 2.70909 ref2: 4.87337 1.32981 -16: pt1: 1.80514 2.32264 pt2: 2.19421 3.23971 +16: ref1: 0.043208 4.46173 ref2: 2.90518 1.43899 +16: pt1: 1.02855 2.81063 pt2: 0.857791 0.388583 16: **************************************** 16: test23D 16: **************************************** @@ -16122,17 +16149,24 @@ 16: **************************************** 16: testFromQuaternion 16: **************************************** - 7/230 Test #16: testTransforms ......................... Passed 0.04 sec + 7/230 Test #16: testTransforms ......................... Passed 0.10 sec test 19 Start 19: testPyGeometry 19: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/Geometry/Wrap/testGeometry.py" 19: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/Geometry/Wrap 19: Test timeout computed to be: 1500 -18: Randomness seeded to: 2873409511 -18: =============================================================================== -18: All tests passed (50 assertions in 5 test cases) -18: +11: Randomness seeded to: 3650614280 +11: =============================================================================== +11: All tests passed (3 assertions in 1 test case) +11: + 8/230 Test #11: catchDataStructs ....................... Passed 0.34 sec +test 20 + Start 20: testMatrices + +20: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/Numerics/testMatrices +20: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/Numerics +20: Test timeout computed to be: 1500 17: *********************************************************** 17: Testing Grid 17: --------------------------------- @@ -16150,59 +16184,17 @@ 17: --------------------------------- 17: testUniformGridIndexing 17: - 8/230 Test #17: testGrid ............................... Passed 0.04 sec - 9/230 Test #18: geometryTestsCatch ..................... Passed 0.03 sec -test 20 - Start 20: testMatrices - -20: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/Numerics/testMatrices -20: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/Numerics -20: Test timeout computed to be: 1500 + 9/230 Test #17: testGrid ............................... Passed 0.12 sec test 21 Start 21: testConrec 21: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/Numerics/testConrec 21: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/Numerics 21: Test timeout computed to be: 1500 -20: [02:22:45] ----------------------------------------- -20: [02:22:45] Testing RDNumerics: vectors and matrices Code -20: [02:22:45] --------------------------------------- -20: [02:22:45] test1Vector -20: [02:22:45] --------------------------------------- -20: [02:22:45] test2Matrix -20: [02:22:45] --------------------------------------- -20: [02:22:45] test3SquareMatrix -20: [02:22:45] --------------------------------------- -20: [02:22:45] test4SymmMatrix - 10/230 Test #20: testMatrices ........................... Passed 0.02 sec -test 22 - Start 22: testAlignment - -22: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/Numerics/Alignment/testAlignment -22: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/Numerics/Alignment -22: Test timeout computed to be: 1500 -22: ----------------------------------------- -22: Testing Alignment Code -22: --------------------------------------- -22: testBasic -22: --------------------------------------- -22: testTriangle -22: --------------------------------------- -22: testFourPts -22: --------------------------------------- -22: testReflection -22: --------------------------------------- - 11/230 Test #22: testAlignment .......................... Passed 0.01 sec -test 23 - Start 23: pyAlignment - -23: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/Numerics/Alignment/Wrap/testAlignment.py" -23: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/Numerics/Alignment/Wrap -23: Test timeout computed to be: 1500 -21: Randomness seeded to: 3957194059 -21: =============================================================================== -21: All tests passed (76 assertions in 3 test cases) -21: +20: [23:09:29] ----------------------------------------- +20: [23:09:29] Testing RDNumerics: vectors and matrices Code +20: [23:09:29] --------------------------------------- +20: [23:09:29] test1Vector 1: core 1: RDKit 2D 1: @@ -16217,26 +16209,8 @@ 1: 4 1 1 0 1: M END 1: - 12/230 Test #21: testConrec ............................. Passed 0.05 sec -test 24 - Start 24: testOptimizer - -24: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/Numerics/Optimizer/testOptimizer -24: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/Numerics/Optimizer -24: Test timeout computed to be: 1500 -24: ------------------------------------- -24: Testing linear search. -24: done -24: ------------------------------------- -24: Testing BFGS optimization. -24: done - 13/230 Test #24: testOptimizer .......................... Passed 0.01 sec -test 25 - Start 25: ForceFieldsCatch - -25: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ForceField/ForceFieldsCatch -25: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ForceField -25: Test timeout computed to be: 1500 +20: [23:09:29] --------------------------------------- +20: [23:09:29] test2Matrix 1: core+sidechain 1: RDKit 2D 1: @@ -16257,13 +16231,6 @@ 1: 7 1 1 0 1: M END 1: - 14/230 Test #10: testMultiFPB ........................... Passed 0.20 sec -test 26 - Start 26: testUFFForceField - -26: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ForceField/UFF/testUFFForceField -26: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ForceField/UFF -26: Test timeout computed to be: 1500 1: templated 1: RDKit 2D 1: @@ -16497,6 +16464,17 @@ 1: 9 5 1 0 1: M END 1: +20: [23:09:29] --------------------------------------- +20: [23:09:29] test3SquareMatrix +20: [23:09:29] --------------------------------------- +20: [23:09:29] test4SymmMatrix + 10/230 Test #20: testMatrices ........................... Passed 0.08 sec +test 22 + Start 22: testAlignment + +22: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/Numerics/Alignment/testAlignment +22: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/Numerics/Alignment +22: Test timeout computed to be: 1500 1: core+sidechain 1: RDKit 2D 1: @@ -16543,10 +16521,6 @@ 1: 11 9 1 0 1: M END 1: -25: Randomness seeded to: 1466371123 -25: =============================================================================== -25: All tests passed (20 assertions in 2 test cases) -25: 1: templated 1: RDKit 2D 1: @@ -16646,52 +16620,6 @@ 1: 5 7 1 0 1: M END 1: -26: ------------------------------------- -26: Unit tests for force field basics. -26: done -26: ------------------------------------- -26: Unit tests for basics of UFF bond-stretch terms. -26: done -26: ------------------------------------- -26: Unit tests for UFF bond-stretch terms. -26: done -26: ------------------------------------- -26: Unit tests for basics of UFF angle terms. -26: done -26: ------------------------------------- -26: Unit tests for UFF angle-bend terms. -26: theta = 3.14159; theta0 = 3.14159 -26: theta = 2.094395, param1.theta0 = 2.094395 -26: done -26: ------------------------------------- -26: Test Simple UFF molecule optimizations. -26: done -26: ------------------------------------- -26: Unit tests for UFF nonbonded terms. -26: done -26: ------------------------------------- -26: Test UFF torsional terms. -26: done -26: ------------------------------------- -26: Test UFF Parameter objects -26: ------------------------------------- -26: Test Simple UFF molecule optimization, part 2. -26: done -26: ------------------------------------- -26: Test UFF Torsion Conflicts. -26: C 0.4783 -0.7477 -0.0753 -26: C -0.5465 -0.0176 0.3519 -26: C -0.5114 1.4472 0.0870 -26: H -1.5201 -0.4838 0.2485 -26: H 0.4696 1.8363 0.3367 -26: O -1.2618 1.9423 0.6934 -26: F -0.7163 1.6298 -0.9622 -26: done -26: ------------------------------------- -26: Unit tests for UFF distance constraint terms. -26: done -26: ------------------------------------- -26: Unit tests for all UFF constraint terms. 1: test1 1: RDKit 2D 1: @@ -16737,23 +16665,116 @@ 1: 2 5 1 0 1: M END 1: - 15/230 Test #25: ForceFieldsCatch ....................... Passed 0.10 sec +22: ----------------------------------------- +22: Testing Alignment Code +22: --------------------------------------- +22: testBasic +22: --------------------------------------- +22: testTriangle +22: --------------------------------------- +22: testFourPts +22: --------------------------------------- +22: testReflection +22: --------------------------------------- + 11/230 Test #22: testAlignment .......................... Passed 0.08 sec +test 23 + Start 23: pyAlignment + +23: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/Numerics/Alignment/Wrap/testAlignment.py" +23: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/Numerics/Alignment/Wrap +23: Test timeout computed to be: 1500 +18: Randomness seeded to: 2960558940 +18: =============================================================================== +18: All tests passed (50 assertions in 5 test cases) +18: + 12/230 Test #18: geometryTestsCatch ..................... Passed 0.37 sec +test 24 + Start 24: testOptimizer + +24: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/Numerics/Optimizer/testOptimizer +24: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/Numerics/Optimizer +24: Test timeout computed to be: 1500 +24: ------------------------------------- +24: Testing linear search. +24: done +24: ------------------------------------- +24: Testing BFGS optimization. +24: done + 13/230 Test #24: testOptimizer .......................... Passed 0.03 sec +test 25 + Start 25: ForceFieldsCatch + +25: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ForceField/ForceFieldsCatch +25: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ForceField +25: Test timeout computed to be: 1500 +21: Randomness seeded to: 2293708712 +21: =============================================================================== +21: All tests passed (76 assertions in 3 test cases) +21: + 14/230 Test #21: testConrec ............................. Passed 0.36 sec +test 26 + Start 26: testUFFForceField + +26: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ForceField/UFF/testUFFForceField +26: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ForceField/UFF +26: Test timeout computed to be: 1500 +25: Randomness seeded to: 1532197558 +25: =============================================================================== +25: All tests passed (20 assertions in 2 test cases) +25: + 15/230 Test #25: ForceFieldsCatch ....................... Passed 0.09 sec test 27 Start 27: testMMFFForceField 27: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ForceField/MMFF/testMMFFForceField 27: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ForceField/MMFF 27: Test timeout computed to be: 1500 -3: dynamic boost any:0.236352 s -27: ------------------------------------- -27: Official MMFF validation suite. +26: ------------------------------------- +26: Unit tests for force field basics. 26: done 26: ------------------------------------- -26: Unit tests for copying UFF ForceFields. +26: Unit tests for basics of UFF bond-stretch terms. 26: done 26: ------------------------------------- -26: Unit test for UFF butane scan. -3: static RDAny:0.027293 s +26: Unit tests for UFF bond-stretch terms. +26: done +26: ------------------------------------- +26: Unit tests for basics of UFF angle terms. +26: done +26: ------------------------------------- +26: Unit tests for UFF angle-bend terms. +26: theta = 3.14159; theta0 = 3.14159 +26: theta = 2.094395, param1.theta0 = 2.094395 +26: done +26: ------------------------------------- +26: Test Simple UFF molecule optimizations. +26: done +26: ------------------------------------- +26: Unit tests for UFF nonbonded terms. +26: done +26: ------------------------------------- +26: Test UFF torsional terms. +26: done +26: ------------------------------------- +26: Test UFF Parameter objects +26: ------------------------------------- +26: Test Simple UFF molecule optimization, part 2. +26: done +26: ------------------------------------- +26: Test UFF Torsion Conflicts. +26: C 0.4783 -0.7477 -0.0753 +26: C -0.5465 -0.0176 0.3519 +26: C -0.5114 1.4472 0.0870 +26: H -1.5201 -0.4838 0.2485 +26: H 0.4696 1.8363 0.3367 +26: O -1.2618 1.9423 0.6934 +26: F -0.7163 1.6298 -0.9622 +26: done +26: ------------------------------------- +26: Unit tests for UFF distance constraint terms. +26: done +26: ------------------------------------- +26: Unit tests for all UFF constraint terms. 1: cyclosporine a 1: RDKit 2D 1: @@ -17022,17 +17043,8 @@ 1: 10 2 1 0 1: M END 1: -23: ..... -23: ---------------------------------------------------------------------- -23: Ran 5 tests in 0.011s -23: -23: OK -23: Testing Alignment Wrapper code: -14: ......... -14: ---------------------------------------------------------------------- -14: Ran 9 tests in 0.025s -14: -14: OK +27: ------------------------------------- +27: Official MMFF validation suite. 1: github 4845 - nan coordinates but no crash 1: RDKit 2D 1: @@ -17125,36 +17137,58 @@ 1: 30 11 1 0 1: M END 1: -19: ........... -19: ---------------------------------------------------------------------- -19: Ran 11 tests in 0.023s -19: -19: OK -19: Testing Geometry wrapper -15: ......... -15: ---------------------------------------------------------------------- -15: Ran 9 tests in 0.057s -15: -15: OK - 16/230 Test #1: testCoordGen ........................... Passed 0.51 sec +3: dynamic boost any:0.236448 s + 16/230 Test #1: testCoordGen ........................... Passed 1.20 sec test 28 Start 28: pyForceFieldConstraints 28: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/ForceField/Wrap/testConstraints.py" 28: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ForceField/Wrap 28: Test timeout computed to be: 1500 +26: done +26: ------------------------------------- +26: Unit tests for copying UFF ForceFields. +26: done +26: ------------------------------------- +26: Unit test for UFF butane scan. +3: static RDAny:0.027472 s +27: +27: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... +14: ......... +14: ---------------------------------------------------------------------- +14: Ran 9 tests in 0.076s +14: +14: OK 13: ...... 13: ---------------------------------------------------------------------- -13: Ran 6 tests in 0.058s +13: Ran 6 tests in 0.032s 13: 13: OK - 17/230 Test #23: pyAlignment ............................ Passed 0.33 sec +23: ..... +23: ---------------------------------------------------------------------- +23: Ran 5 tests in 0.014s +23: +23: OK +23: Testing Alignment Wrapper code: +15: ......... +15: ---------------------------------------------------------------------- +15: Ran 9 tests in 0.121s +15: +15: OK +26: done + 17/230 Test #26: testUFFForceField ...................... Passed 0.70 sec test 29 Start 29: testDistGeom 29: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/DistGeom/testDistGeom 29: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/DistGeom 29: Test timeout computed to be: 1500 +19: ........... +19: ---------------------------------------------------------------------- +19: Ran 11 tests in 0.091s +19: +19: OK +19: Testing Geometry wrapper 29: *********************************************************** 29: test1 29: *********************************************************** @@ -17166,15 +17200,15 @@ 29: 1 1 1 0 29: *********************************************************** 29: - 18/230 Test #29: testDistGeom ........................... Passed 0.02 sec + 18/230 Test #29: testDistGeom ........................... Passed 0.05 sec test 30 Start 30: pyDistGeom 30: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/DistGeom/Wrap/rough_test.py" 30: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/DistGeom/Wrap 30: Test timeout computed to be: 1500 - 19/230 Test #14: pySparseIntVect ........................ Passed 0.47 sec - 20/230 Test #15: pyFPB .................................. Passed 0.46 sec + 19/230 Test #13: pyDiscreteValueVect .................... Passed 1.46 sec + 20/230 Test #14: pySparseIntVect ........................ Passed 1.42 sec test 31 Start 31: graphmolTest1 @@ -17187,7 +17221,7 @@ 32: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolcpTest 32: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol 32: Test timeout computed to be: 1500 - 21/230 Test #19: testPyGeometry ......................... Passed 0.44 sec + 21/230 Test #23: pyAlignment ............................ Passed 1.05 sec test 33 Start 33: graphmolqueryTest @@ -17198,6 +17232,14 @@ 32: 32: 32: COPY +33: [23:09:30] ---------------------- Test1 + 22/230 Test #32: graphmolcpTest ......................... Passed 0.07 sec +test 34 + Start 34: graphmolMolOpsTest + +34: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolMolOpsTest +34: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol +34: Test timeout computed to be: 1500 31: Atoms: 31: 0 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: 31: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: @@ -17216,9 +17258,58 @@ 31: 4 5->6 order: 3 31: 5 6->7 order: 1 31: 6 7->8 order: 2 -31: [02:22:45] +33: [23:09:30] Done! +33: [23:09:30] ---------------------- Test2 +33: [23:09:30] Done! +33: [23:09:30] ---------------------- Test3 +31: [23:09:30] 31: 31: **** +33: [23:09:30] Done! +33: [23:09:30] ---------------------- Test4 +33: [23:09:30] Done! +33: [23:09:30] ---------------------- Test5 +33: [23:09:30] Done! +33: [23:09:30] Done! +33: [23:09:30] ---------------------- Test issue 2892580 +33: [23:09:30] Done! +33: [23:09:30] ---------------------- Test github issue 53: query molecules not matching [R] +33: [23:09:30] Done! +33: [23:09:30] ---------------------- Test queries using qualifiers instead of == +33: [23:09:30] Done! +33: [23:09:30] ---------------------- Test Github issue 165: radicals not used in atom-atom matching +33: [23:09:30] Done! +33: [23:09:30] ---------------------- Test extra atom queries +33: [23:09:30] Done! +33: [23:09:30] ---------------------- Test extra bond queries +33: [23:09:30] Done! +33: [23:09:30] ---------------------- Test num heteroatom neighbor queries +33: [23:09:30] Done! +33: [23:09:30] ---------------------- Test atom type queries +33: [23:09:30] Done! +33: [23:09:30] ---------------------- Test Github #2471: dummy atom queries are flagged as complex +33: [23:09:30] Done! +33: [23:09:30] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() +33: [23:09:30] Done! +2: .... +2: ---------------------------------------------------------------------- +2: Ran 4 tests in 0.077s +2: +2: OK + 23/230 Test #15: pyFPB .................................. Passed 1.42 sec + 24/230 Test #33: graphmolqueryTest ...................... Passed 0.06 sec +test 35 + Start 35: graphmoltestChirality + +35: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmoltestChirality +35: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol +35: Test timeout computed to be: 1500 +test 36 + Start 36: graphmoltestPickler + +36: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmoltestPickler +36: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol +36: Test timeout computed to be: 1500 31: Pre-condition Violation 31: bond already exists 31: Violation occurred on line 499 in file ./Code/GraphMol/RWMol.cpp @@ -17228,15 +17319,15 @@ 31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -31: 3# 0x0000AAAAC5B2B040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 4# 0x0000AAAAC5B2367C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 5# 0x0000FFFF954A229C in /lib/aarch64-linux-gnu/libc.so.6 +31: 3# 0x0000AAAAB1E4B040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 4# 0x0000AAAAB1E4367C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 5# 0x0000FFFFB38B229C in /lib/aarch64-linux-gnu/libc.so.6 31: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -31: 7# 0x0000AAAAC5B23770 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 7# 0x0000AAAAB1E43770 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 31: ---------- 31: **** 31: -31: [02:22:45] +31: [23:09:30] 31: 31: **** 31: Pre-condition Violation @@ -17248,15 +17339,15 @@ 31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -31: 3# 0x0000AAAAC5B2B260 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 4# 0x0000AAAAC5B2367C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 5# 0x0000FFFF954A229C in /lib/aarch64-linux-gnu/libc.so.6 +31: 3# 0x0000AAAAB1E4B260 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 4# 0x0000AAAAB1E4367C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 5# 0x0000FFFFB38B229C in /lib/aarch64-linux-gnu/libc.so.6 31: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -31: 7# 0x0000AAAAC5B23770 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 7# 0x0000AAAAB1E43770 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 31: ---------- 31: **** 31: -31: [02:22:45] +31: [23:09:30] 31: 31: **** 31: Pre-condition Violation @@ -17268,15 +17359,15 @@ 31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -31: 3# 0x0000AAAAC5B2B354 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 4# 0x0000AAAAC5B2367C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 5# 0x0000FFFF954A229C in /lib/aarch64-linux-gnu/libc.so.6 +31: 3# 0x0000AAAAB1E4B354 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 4# 0x0000AAAAB1E4367C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 5# 0x0000FFFFB38B229C in /lib/aarch64-linux-gnu/libc.so.6 31: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -31: 7# 0x0000AAAAC5B23770 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 7# 0x0000AAAAB1E43770 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 31: ---------- 31: **** 31: -31: [02:22:45] +31: [23:09:30] 31: 31: **** 31: Pre-condition Violation @@ -17288,15 +17379,15 @@ 31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -31: 3# 0x0000AAAAC5B2B394 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 4# 0x0000AAAAC5B2367C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 5# 0x0000FFFF954A229C in /lib/aarch64-linux-gnu/libc.so.6 +31: 3# 0x0000AAAAB1E4B394 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 4# 0x0000AAAAB1E4367C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 5# 0x0000FFFFB38B229C in /lib/aarch64-linux-gnu/libc.so.6 31: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -31: 7# 0x0000AAAAC5B23770 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 7# 0x0000AAAAB1E43770 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 31: ---------- 31: **** 31: -31: [02:22:45] +31: [23:09:30] 31: 31: **** 31: Pre-condition Violation @@ -17308,62 +17399,27 @@ 31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -31: 3# 0x0000AAAAC5B2B4DC in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 4# 0x0000AAAAC5B2367C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 5# 0x0000FFFF954A229C in /lib/aarch64-linux-gnu/libc.so.6 +31: 3# 0x0000AAAAB1E4B4DC in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 4# 0x0000AAAAB1E4367C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 5# 0x0000FFFFB38B229C in /lib/aarch64-linux-gnu/libc.so.6 31: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -31: 7# 0x0000AAAAC5B23770 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 7# 0x0000AAAAB1E43770 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 31: ---------- 31: **** 31: -31: [02:22:45] Explicit valence for atom # 0 B, 4, is greater than permitted -31: [02:22:45] Explicit valence for atom # 0 B, 4, is greater than permitted -33: [02:22:45] ---------------------- Test1 - 22/230 Test #32: graphmolcpTest ......................... Passed 0.03 sec -test 34 - Start 34: graphmolMolOpsTest - -34: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolMolOpsTest -34: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol -34: Test timeout computed to be: 1500 -33: [02:22:45] Done! -33: [02:22:45] ---------------------- Test2 -33: [02:22:45] Done! -33: [02:22:45] ---------------------- Test3 -33: [02:22:45] Done! -33: [02:22:45] ---------------------- Test4 -33: [02:22:45] Done! -33: [02:22:45] ---------------------- Test5 -33: [02:22:45] Done! -33: [02:22:45] Done! -33: [02:22:45] ---------------------- Test issue 2892580 -33: [02:22:45] Done! -33: [02:22:45] ---------------------- Test github issue 53: query molecules not matching [R] -33: [02:22:45] Done! -33: [02:22:45] ---------------------- Test queries using qualifiers instead of == -33: [02:22:45] Done! -33: [02:22:45] ---------------------- Test Github issue 165: radicals not used in atom-atom matching -33: [02:22:45] Done! -33: [02:22:45] ---------------------- Test extra atom queries -33: [02:22:45] Done! -33: [02:22:45] ---------------------- Test extra bond queries -33: [02:22:45] Done! -33: [02:22:45] ---------------------- Test num heteroatom neighbor queries -33: [02:22:45] Done! -33: [02:22:45] ---------------------- Test atom type queries -33: [02:22:45] Done! -33: [02:22:45] ---------------------- Test Github #2471: dummy atom queries are flagged as complex -33: [02:22:45] Done! -33: [02:22:45] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() -33: [02:22:45] Done! - 23/230 Test #33: graphmolqueryTest ...................... Passed 0.04 sec -test 35 - Start 35: graphmoltestChirality +31: [23:09:30] Explicit valence for atom # 0 B, 4, is greater than permitted +31: [23:09:30] Explicit valence for atom # 0 B, 4, is greater than permitted + 25/230 Test #19: testPyGeometry ......................... Passed 1.35 sec +test 37 + Start 37: graphmoltestPicklerGlobalSetting -35: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmoltestChirality -35: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol -35: Test timeout computed to be: 1500 -31: [02:22:45] +37: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmoltestPicklerGlobalSetting +37: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol +37: Test timeout computed to be: 1500 +34: 1 1 2 +34: 1 1 1 +34: 2 1 0.75 +31: [23:09:30] 31: 31: **** 31: Post-condition Violation @@ -17375,48 +17431,29 @@ 31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 3# 0x0000AAAAC5B56048 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 4# 0x0000AAAAC5B39BF8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 5# 0x0000AAAAC5B23688 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 6# 0x0000FFFF954A229C in /lib/aarch64-linux-gnu/libc.so.6 +31: 3# 0x0000AAAAB1E76048 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 4# 0x0000AAAAB1E59BF8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 5# 0x0000AAAAB1E43688 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 6# 0x0000FFFFB38B229C in /lib/aarch64-linux-gnu/libc.so.6 31: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -31: 8# 0x0000AAAAC5B23770 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 8# 0x0000AAAAB1E43770 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 31: ---------- 31: **** 31: -31: [02:22:45] ------------------------------------- -31: [02:22:45] Test github381: thread-safe initialization of the periodic table -26: done - 24/230 Test #26: testUFFForceField ...................... Passed 0.40 sec -test 36 - Start 36: graphmoltestPickler - -36: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmoltestPickler -36: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol -36: Test timeout computed to be: 1500 -2: .... -2: ---------------------------------------------------------------------- -2: Ran 4 tests in 0.046s -2: -2: OK -27: -27: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... - 25/230 Test #13: pyDiscreteValueVect .................... Passed 0.58 sec -test 37 - Start 37: graphmoltestPicklerGlobalSetting - -37: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmoltestPicklerGlobalSetting -37: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol -37: Test timeout computed to be: 1500 +31: [23:09:30] ------------------------------------- +31: [23:09:30] Test github381: thread-safe initialization of the periodic table +36: [23:09:30] ------------------------------------- +36: [23:09:30] Testing String Pickle Roundtrips. +34: path: 2 +34: [23:09:30] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored +34: [23:09:30] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored 35: -------------------------- 35: -------------------------- 35: C/C=C/C(C)Cl -36: [02:22:45] ------------------------------------- -36: [02:22:45] Testing String Pickle Roundtrips. -31: [02:22:45] done -31: [02:22:45] ------------------------------------- -31: [02:22:45] Test github1041: Segfault for atom with no owner (expect some warnings) -31: [02:22:45] +31: [23:09:30] done +31: [23:09:30] ------------------------------------- +31: [23:09:30] Test github1041: Segfault for atom with no owner (expect some warnings) +31: [23:09:30] 31: 31: **** 31: Pre-condition Violation @@ -17427,15 +17464,15 @@ 31: Stacktrace: 31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -31: 2# 0x0000AAAAC5B4A2D8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 3# 0x0000AAAAC5B236AC in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 4# 0x0000FFFF954A229C in /lib/aarch64-linux-gnu/libc.so.6 +31: 2# 0x0000AAAAB1E6A2D8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 3# 0x0000AAAAB1E436AC in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 4# 0x0000FFFFB38B229C in /lib/aarch64-linux-gnu/libc.so.6 31: 5# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -31: 6# 0x0000AAAAC5B23770 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 6# 0x0000AAAAB1E43770 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 31: ---------- 31: **** 31: -31: [02:22:45] +31: [23:09:30] 31: 31: **** 31: Pre-condition Violation @@ -17446,18 +17483,18 @@ 31: Stacktrace: 31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -31: 2# 0x0000AAAAC5B4A6B4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 3# 0x0000AAAAC5B236AC in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 4# 0x0000FFFF954A229C in /lib/aarch64-linux-gnu/libc.so.6 +31: 2# 0x0000AAAAB1E6A6B4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 3# 0x0000AAAAB1E436AC in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 4# 0x0000FFFFB38B229C in /lib/aarch64-linux-gnu/libc.so.6 31: 5# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -31: 6# 0x0000AAAAC5B23770 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 6# 0x0000AAAAB1E43770 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 31: ---------- 31: **** 31: -31: [02:22:45] done -31: [02:22:45] ------------------------------------- -31: [02:22:45] Test github1041: Segfault for atom with no owner (expect some warnings) -31: [02:22:45] +31: [23:09:30] done +31: [23:09:30] ------------------------------------- +31: [23:09:30] Test github1041: Segfault for atom with no owner (expect some warnings) +31: [23:09:30] 31: 31: **** 31: Pre-condition Violation @@ -17468,15 +17505,15 @@ 31: Stacktrace: 31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -31: 2# 0x0000AAAAC5B4A2D8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 3# 0x0000AAAAC5B236B0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 4# 0x0000FFFF954A229C in /lib/aarch64-linux-gnu/libc.so.6 +31: 2# 0x0000AAAAB1E6A2D8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 3# 0x0000AAAAB1E436B0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 4# 0x0000FFFFB38B229C in /lib/aarch64-linux-gnu/libc.so.6 31: 5# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -31: 6# 0x0000AAAAC5B23770 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 6# 0x0000AAAAB1E43770 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 31: ---------- 31: **** 31: -31: [02:22:45] +31: [23:09:30] 31: 31: **** 31: Pre-condition Violation @@ -17487,96 +17524,84 @@ 31: Stacktrace: 31: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 31: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -31: 2# 0x0000AAAAC5B4A6B4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 3# 0x0000AAAAC5B236B0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -31: 4# 0x0000FFFF954A229C in /lib/aarch64-linux-gnu/libc.so.6 +31: 2# 0x0000AAAAB1E6A6B4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 3# 0x0000AAAAB1E436B0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 4# 0x0000FFFFB38B229C in /lib/aarch64-linux-gnu/libc.so.6 31: 5# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -31: 6# 0x0000AAAAC5B23770 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +31: 6# 0x0000AAAAB1E43770 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 31: ---------- 31: **** 31: -31: [02:22:45] done -31: [02:22:45] ------------------------------------- -31: [02:22:45] Test github1453: RWMol.clear() should reset the numBonds count. -31: [02:22:45] done -31: [02:22:45] ------------------------------------- -31: [02:22:45] Test range-based for loops. -31: [02:22:45] done -31: [02:22:45] ------------------------------------- -31: [02:22:45] Test github1642: Atom index type is too low for big molecules. -37: [02:22:45] done - 26/230 Test #37: graphmoltestPicklerGlobalSetting ....... Passed 0.03 sec +31: [23:09:30] done +31: [23:09:30] ------------------------------------- +31: [23:09:30] Test github1453: RWMol.clear() should reset the numBonds count. +31: [23:09:30] done +31: [23:09:30] ------------------------------------- +31: [23:09:30] Test range-based for loops. +31: [23:09:30] done +31: [23:09:30] ------------------------------------- +31: [23:09:30] Test github1642: Atom index type is too low for big molecules. +34: [23:09:30] Explicit valence for atom # 0 B, 5, is greater than permitted +34: [23:09:30] Explicit valence for atom # 1 C, 5, is greater than permitted +34: [23:09:30] Explicit valence for atom # 1 C, 5, is greater than permitted +34: [23:09:30] Explicit valence for atom # 1 C, 5, is greater than permitted +34: [23:09:30] Explicit valence for atom # 1 Si, 7, is greater than permitted +37: [23:09:30] done + 26/230 Test #37: graphmoltestPicklerGlobalSetting ....... Passed 0.09 sec test 38 Start 38: graphmolIterTest 38: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolIterTest 38: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol 38: Test timeout computed to be: 1500 -3: dynamic RDAny:0.231437 s -3: static RDValue:1e-06 s -35: [02:22:45] Conflicting single bond directions around double bond at index 2. -35: [02:22:45] BondStereo set to STEREONONE and single bond directions set to NONE. -35: [02:22:45] Conflicting single bond directions around double bond at index 4. -35: [02:22:45] BondStereo set to STEREONONE and single bond directions set to NONE. -35: [02:22:45] Conflicting single bond directions around double bond at index 15. -35: [02:22:45] BondStereo set to STEREONONE and single bond directions set to NONE. -35: [02:22:45] Conflicting single bond directions around double bond at index 2. -35: [02:22:45] BondStereo set to STEREONONE and single bond directions set to NONE. -35: [02:22:45] Conflicting single bond directions around double bond at index 1. -35: [02:22:45] BondStereo set to STEREONONE and single bond directions set to NONE. -34: 1 1 2 -34: 1 1 1 -34: 2 1 0.75 -34: path: 2 -36: [02:22:45] done -36: [02:22:45] ------------------------------------- -36: [02:22:45] Testing reading existing pickle file (v2). - 27/230 Test #38: graphmolIterTest ....................... Passed 0.04 sec +35: [23:09:30] Conflicting single bond directions around double bond at index 2. +35: [23:09:30] BondStereo set to STEREONONE and single bond directions set to NONE. +35: [23:09:30] Conflicting single bond directions around double bond at index 4. +35: [23:09:30] BondStereo set to STEREONONE and single bond directions set to NONE. +35: [23:09:30] Conflicting single bond directions around double bond at index 15. +35: [23:09:30] BondStereo set to STEREONONE and single bond directions set to NONE. +35: [23:09:30] Conflicting single bond directions around double bond at index 2. +35: [23:09:30] BondStereo set to STEREONONE and single bond directions set to NONE. +35: [23:09:30] Conflicting single bond directions around double bond at index 1. +35: [23:09:30] BondStereo set to STEREONONE and single bond directions set to NONE. +35: -------------------------------------------------- + 27/230 Test #35: graphmoltestChirality .................. Passed 0.18 sec test 39 Start 39: hanoiTest 39: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/hanoiTest 39: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol 39: Test timeout computed to be: 1500 -39: [02:22:45] Testing the hanoi sort -39: [02:22:45] populating vectors -35: -------------------------------------------------- -3: dynamic RDValue:0.033501 s - 28/230 Test #35: graphmoltestChirality .................. Passed 0.14 sec + 28/230 Test #38: graphmolIterTest ....................... Passed 0.08 sec test 40 Start 40: graphmolMemTest1 40: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolMemTest1 40: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol 40: Test timeout computed to be: 1500 -34: [02:22:45] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored -34: [02:22:45] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored - 29/230 Test #40: graphmolMemTest1 ....................... Passed 0.01 sec +36: [23:09:30] done +36: [23:09:30] ------------------------------------- +36: [23:09:30] Testing reading existing pickle file (v2). +39: [23:09:30] Testing the hanoi sort +39: [23:09:30] populating vectors + 29/230 Test #40: graphmolMemTest1 ....................... Passed 0.04 sec test 41 Start 41: resMolSupplierTest 41: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/resMolSupplierTest 41: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol 41: Test timeout computed to be: 1500 -3: deleted! -3: [02:22:45] ------------------------------------- -3: [02:22:45] Testing String Pickle Roundtrips. -3: [02:22:45] done -3: [02:22:45] ------------------------------------- -3: [02:22:45] Testing conversion of vect to string. -3: [02:22:45] done -3: [02:22:45] ------------------------------------- -3: [02:22:45] Testing returning const references. -3: [02:22:45] any cast -3: [02:22:45] done: 0.000773 300000 -3: [02:22:45] copy -3: [02:22:45] done: 0.000823 300000 -3: [02:22:45] ref -3: [02:22:45] done: 0.000778 300000 -3: [02:22:45] dict -36: [02:22:45] done -36: [02:22:45] ------------------------------------- -36: [02:22:45] Testing combining molecules using pickles. +34: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 + 30/230 Test #2: pyCoordGen ............................. Passed 2.14 sec +test 42 + Start 42: molBundleTest + +42: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/molBundleTest +42: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol +42: Test timeout computed to be: 1500 +36: [23:09:31] done +36: [23:09:31] ------------------------------------- +36: [23:09:31] Testing combining molecules using pickles. 36: Atoms: 36: 0 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 36: 1 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 @@ -17593,62 +17618,44 @@ 36: 4 4->5 order: 1 36: 5 5->6 order: 1 36: 6 6->3 order: 1 -36: [02:22:45] done -36: [02:22:45] ------------------------------------- -36: [02:22:45] Testing Issue164: Roundtrip Pickle Failure. -34: [02:22:45] Explicit valence for atom # 0 B, 5, is greater than permitted -34: [02:22:45] Explicit valence for atom # 1 C, 5, is greater than permitted -34: [02:22:45] Explicit valence for atom # 1 C, 5, is greater than permitted -34: [02:22:45] Explicit valence for atom # 1 C, 5, is greater than permitted -34: [02:22:45] Explicit valence for atom # 1 Si, 7, is greater than permitted -3: [02:22:45] done: 0.001909 300000 -3: [02:22:45] ref with hasVal -3: [02:22:45] done: 0.001239 300000 -3: [02:22:45] done -3: [02:22:45] ------------------------------------- -3: [02:22:45] Testing dict update. -3: [02:22:45] done -3: deleted! -3: deleted! -3: deleted! -3: deleted! -3: deleted! -3: deleted! - 30/230 Test #3: testDict ............................... Passed 0.80 sec -test 42 - Start 42: molBundleTest - -42: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/molBundleTest -42: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol -42: Test timeout computed to be: 1500 -36: [02:22:45] done -36: [02:22:45] ------------------------------------- -36: [02:22:45] Testing Issue219: Pickle Failure with Conformations. -36: [02:22:45] done -36: [02:22:45] ------------------------------------- -36: [02:22:45] Testing Issue220: Pickle problems with bond stereochemistry. -36: [02:22:45] done -36: [02:22:45] ------------------------------------- -36: [02:22:45] Testing query serialization. -36: [02:22:45] C=[$(C=O)] -36: [02:22:45] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] -36: [02:22:45] done -36: [02:22:45] ------------------------------------- -36: [02:22:45] Testing radical handling in pickles. -36: [02:22:45] done -36: [02:22:45] done -36: [02:22:45] ------------------------------------- -36: [02:22:45] Testing sf.net issue 2788233. -36: [02:22:45] done -36: [02:22:45] ------------------------------------- -36: [02:22:45] Testing sf.net issue 3202580. +36: [23:09:31] done +36: [23:09:31] ------------------------------------- +36: [23:09:31] Testing Issue164: Roundtrip Pickle Failure. +34: [23:09:31] non-ring atom 0 marked aromatic +34: [23:09:31] non-ring atom 0 marked aromatic +36: [23:09:31] done +36: [23:09:31] ------------------------------------- +36: [23:09:31] Testing Issue219: Pickle Failure with Conformations. +36: [23:09:31] done +36: [23:09:31] ------------------------------------- +36: [23:09:31] Testing Issue220: Pickle problems with bond stereochemistry. +36: [23:09:31] done +36: [23:09:31] ------------------------------------- +36: [23:09:31] Testing query serialization. +36: [23:09:31] C=[$(C=O)] +36: [23:09:31] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] +36: [23:09:31] done +36: [23:09:31] ------------------------------------- +36: [23:09:31] Testing radical handling in pickles. +36: [23:09:31] done +36: [23:09:31] done +36: [23:09:31] ------------------------------------- +36: [23:09:31] Testing sf.net issue 2788233. +36: [23:09:31] done +36: [23:09:31] ------------------------------------- +36: [23:09:31] Testing sf.net issue 3202580. 36: mass! 13.0034 -36: [02:22:45] done -36: [02:22:45] ------------------------------------- -36: [02:22:45] Testing sf.net issue 3316407. -36: [02:22:45] done -36: [02:22:45] ------------------------------------- -36: [02:22:45] Testing sf.net issue 3496759. +36: [23:09:31] done +36: [23:09:31] ------------------------------------- +36: [23:09:31] Testing sf.net issue 3316407. +34: [23:09:31] Conflicting single bond directions around double bond at index 17. +34: [23:09:31] BondStereo set to STEREONONE and single bond directions set to NONE. +34: starting ring finding +34: done +34: starting ring finding +36: [23:09:31] done +36: [23:09:31] ------------------------------------- +36: [23:09:31] Testing sf.net issue 3496759. 36: smi match: *C *C 36: smi match: **=* **=* 36: smi match: [N-]=[N+]=NC=O [N-]=[N+]=NC=O @@ -17680,6 +17687,15 @@ 36: smi match: CCOP(=O)(C#N)OCC CCOP(=O)(C#N)OCC 36: smi match: N#CN=N N#CN=N 36: smi match: N=NCC=O N=NCC=O +3: dynamic RDAny:0.232426 s +3: static RDValue:0 s + 31/230 Test #42: molBundleTest .......................... Passed 0.08 sec +test 43 + Start 43: testSGroup + +43: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/testSGroup +43: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol +43: Test timeout computed to be: 1500 36: smi match: CCCCCCC CCCCCCC 36: smi match: OCCOCCO OCCOCCO 36: smi match: SS SS @@ -17704,6 +17720,12 @@ 36: smi match: [OH]C1Cc2c([OH])cc([OH])cc2OC1c1ccc([OH])c([OH])c1 [OH]C1Cc2c([OH])cc([OH])cc2OC1c1ccc([OH])c([OH])c1 36: smi match: C1CC2CCC(O1)O2 C1CC2CCC(O1)O2 36: smi match: cN(=O)~O cN(=O)~O +34: done +34: starting ring finding +34: done +34: C/C=N/c1ccc(cc1)c1cc2cc(c1)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)C)c1ccc(cc1)C=Nc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)/N=C/C)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(c3ccc(C=Nc4ccc(c5cc6c7ccc(N=Cc8ccc(c9cc(c%10ccc(C=Nc%11ccc2cc%11)cc%10)cc(c9)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)N=Cc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)C)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(c9ccc(N=Cc%10ccc(c%11cc(c%12ccc(C=Nc%13ccc(c(c6)c5)cc%13)cc%12)cc(c%11)c5ccc(cc5)C)cc%10)cc9)cc(c2)c2ccc(cc2)/N=C/C)c2ccc(cc2)/N=C/C)cc8)cc7)cc4)cc3)cc(c1)c1ccc(cc1)C +34: starting sanitization +28: ...[23:09:31] Molecule does not have explicit Hs. Consider calling AddHs() 36: smi match: *[CH2]N1C(=O)CCC1=O *[CH2]N1C(=O)CCC1=O 36: smi match: N~NC=O N~NC=O 36: smi match: *=N~C *=N~C @@ -17749,13 +17771,6 @@ 36: smi match: C=CC(=S)S C=CC(=S)S 36: smi match: *C=C(*)C=C *C=C(*)C=C 36: smi match: C=CC=N C=CC=N - 31/230 Test #42: molBundleTest .......................... Passed 0.04 sec -test 43 - Start 43: testSGroup - -43: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/testSGroup -43: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol -43: Test timeout computed to be: 1500 36: smi match: *N(*)C=C *N(*)C=C 36: smi match: C=CN(=O)=O C=CN(=O)=O 36: smi match: C=CN(O)=O C=CN(O)=O @@ -17768,6 +17783,8 @@ 36: smi match: C=NN C=NN 36: smi match: C=NN=C C=NN=C 36: smi match: C=NO C=NO +34: done +34: starting sanitization 36: smi match: C=NOC=O C=NOC=O 36: smi match: C=N=O C=N=O 36: smi match: N#CS N#CS @@ -17812,6 +17829,12 @@ 36: smi match: *C(c)O *C(c)O 36: smi match: C=CS(c)(=O)=O C=CS(c)(=O)=O 36: smi match: cS(=O)(=O)O cS(=O)(=O)O +34: done +34: starting ring finding +34: done +34: starting ring finding +34: done +34: smiles: CC[C@]1(C(=O)c([nH])n)CC[C@](C)(O)CC1 36: smi match: *c1ccccn1=O *c1ccccn1=O 36: smi match: *c1ccccn1 *c1ccccn1 36: smi match: *c1nccccn1 *c1nccccn1 @@ -17848,18 +17871,6 @@ 36: smi match: C=CN C=CN 36: smi match: C=N[SH](=O)=O C=N[SH](=O)=O 36: smi match: NN=O NN=O -30: ...... -30: ---------------------------------------------------------------------- -30: Ran 6 tests in 0.010s -30: -30: OK - 32/230 Test #2: pyCoordGen ............................. Passed 0.86 sec -test 44 - Start 44: test-valgrind - -44: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/test-valgrind -44: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol -44: Test timeout computed to be: 1500 36: smi match: NC(=O)S NC(=O)S 36: smi match: N#CS N#CS 36: smi match: NC(=O)C(N)=O NC(=O)C(N)=O @@ -17867,6 +17878,13 @@ 36: smi match: C1COCO1 C1COCO1 36: smi match: C=NN[SH](=O)=O C=NN[SH](=O)=O 36: smi match: O=CC=O O=CC=O + 32/230 Test #43: testSGroup ............................. Passed 0.08 sec +test 44 + Start 44: test-valgrind + +44: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/test-valgrind +44: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol +44: Test timeout computed to be: 1500 36: smi match: O=CNOC=O O=CNOC=O 36: smi match: O=C1C=CC(=O)C=C1 O=C1C=CC(=O)C=C1 36: smi match: ONO ONO @@ -17933,6 +17951,10 @@ 36: smi match: *C(*)[SH](=O)=O *C(*)[SH](=O)=O 36: smi match: *C[SH](=O)=O *C[SH](=O)=O 36: smi match: * * +34: [23:09:31] WARNING: not removing hydrogen atom with dummy atom neighbors +3: dynamic RDValue:0.033837 s +34: ------------------------------- +34: [23:09:31] Explicit valence for atom # 0 N, 4, is greater than permitted 36: smi match: *1CC1 *1CC1 36: smi match: O=COC=O O=COC=O 36: smi match: N=C=O N=C=O @@ -17967,6 +17989,16 @@ 36: smi match: SS SS 36: smi match: [SH] [SH] 36: smi match: *C* *C* +3: deleted! +34: [23:09:31] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +34: [23:09:31] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +34: [23:09:31] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +34: [23:09:31] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +3: [23:09:31] ------------------------------------- +3: [23:09:31] Testing String Pickle Roundtrips. +3: [23:09:31] done +3: [23:09:31] ------------------------------------- +3: [23:09:31] Testing conversion of vect to string. 36: smi match: * * 36: smi match: C[nH3+] C[nH3+] 36: smi match: cC(=N)[NH2] cC(=N)[NH2] @@ -17990,15 +18022,38 @@ 36: smi match: C[OH] C[OH] 36: smi match: C[CH]=O C[CH]=O 36: smi match: *=* *=* - 33/230 Test #44: test-valgrind .......................... Passed 0.03 sec +36: smi match: *C *C +36: smi match: C#C C#C +3: [23:09:31] done +3: [23:09:31] ------------------------------------- +3: [23:09:31] Testing returning const references. +3: [23:09:31] any cast +3: [23:09:31] done: 0.000768 300000 +3: [23:09:31] copy +3: [23:09:31] done: 0.000801 300000 +3: [23:09:31] ref +3: [23:09:31] done: 0.000767 300000 +3: [23:09:31] dict +3: [23:09:31] done: 0.001941 300000 +3: [23:09:31] ref with hasVal +3: [23:09:31] done: 0.001235 300000 +3: [23:09:31] done +3: [23:09:31] ------------------------------------- +3: [23:09:31] Testing dict update. +3: [23:09:31] done +3: deleted! +3: deleted! +3: deleted! +3: deleted! +3: deleted! +3: deleted! + 33/230 Test #3: testDict ............................... Passed 2.36 sec test 45 Start 45: graphmolTestsCatch 45: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol 45: Test timeout computed to be: 1500 -36: smi match: *C *C -36: smi match: C#C C#C 36: smi match: *[CH]C=C *[CH]C=C 36: smi match: cCC(=O)[OH] cCC(=O)[OH] 36: smi match: *C(*)(*)C(=O)[OH] *C(*)(*)C(=O)[OH] @@ -18039,12 +18094,19 @@ 36: smi match: *OC(=O)O* *OC(=O)O* 36: smi match: * * 36: smi match: *OC(=O)Cl *OC(=O)Cl -28: ...[02:22:46] Molecule does not have explicit Hs. Consider calling AddHs() 36: smi match: *C#N *C#N 36: smi match: NCC(=O)NCC=O NCC(=O)NCC=O 36: smi match: SS SS 36: smi match: * * 36: smi match: *=* *=* +34: [23:09:31] WARNING: not removing hydrogen atom with dummy atom neighbors + 34/230 Test #44: test-valgrind .......................... Passed 0.11 sec +test 46 + Start 46: graphmolOrganometallicsCatch + +46: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolOrganometallicsCatch +46: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol +46: Test timeout computed to be: 1500 36: smi match: *=* *=* 36: smi match: *=* *=* 36: smi match: *=* *=* @@ -18102,101 +18164,90 @@ 36: smi match: * * 36: smi match: ***** ***** 36: smi match: NC(N)=O NC(N)=O -36: [02:22:46] done -36: [02:22:46] ------------------------------------- -36: [02:22:46] Testing sf.net issue 280. -36: [02:22:46] done -36: [02:22:46] ------------------------------------- -36: [02:22:46] Testing sf.net issue 285. -36: [02:22:46] done -36: [02:22:46] done -36: [02:22:46] done -36: [02:22:46] done -36: [02:22:46] done -36: [02:22:46] done -36: [02:22:46] done -36: [02:22:46] ------------------------------------- -36: [02:22:46] Testing Github2441: Add RDProps interface to Conformers. -36: [02:22:46] done -36: [02:22:46] ------------------------------------- -36: [02:22:46] Testing Issue2510: Pickle Confs as double. -36: [02:22:46] done -36: [02:22:46] ------------------------------------- -36: [02:22:46] Testing Github #2465: Negative atom-map numbers cause depickling to fail. -36: [02:22:46] done -36: [02:22:46] ------------------------------------- -36: [02:22:46] Testing loading pickled mols with conformers -36: [02:22:46] done -36: [02:22:46] ------------------------------------- -36: [02:22:46] Testing conformer reading/writing options -36: [02:22:46] done -36: [02:22:46] ------------------------------------- -36: [02:22:46] Testing property reading options -36: [02:22:46] done -36: [02:22:46] ------------------------------------- -36: [02:22:46] Testing property reading options -36: [02:22:46] done -36: [02:22:46] ------------------------------------- -36: [02:22:46] Testing boost::serialization integration - 34/230 Test #30: pyDistGeom ............................. Passed 0.37 sec -test 46 - Start 46: graphmolOrganometallicsCatch - -46: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolOrganometallicsCatch -46: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol -46: Test timeout computed to be: 1500 -45: Randomness seeded to: 2870237286 -45: [02:22:46] WARNING: not removing hydrogen atom without neighbors -45: [02:22:46] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -45: [02:22:46] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -45: [02:22:46] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -45: [02:22:46] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -45: [02:22:46] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -45: [02:22:46] Explicit valence for atom # 1 N, 5, is greater than permitted -45: [02:22:46] Explicit valence for atom # 1 N, 6, is greater than permitted -45: [02:22:46] Explicit valence for atom # 1 N, 5, is greater than permitted -45: [02:22:46] Explicit valence for atom # 1 N, 5, is greater than permitted -36: [02:22:46] done -36: [02:22:46] ------------------------------------- -36: [02:22:46] Testing github issue 6036 - 35/230 Test #36: graphmoltestPickler .................... Passed 0.28 sec +36: [23:09:31] done +36: [23:09:31] ------------------------------------- +36: [23:09:31] Testing sf.net issue 280. +36: [23:09:31] done +36: [23:09:31] ------------------------------------- +36: [23:09:31] Testing sf.net issue 285. +36: [23:09:31] done +36: [23:09:31] done +36: [23:09:31] done +36: [23:09:31] done +36: [23:09:31] done +36: [23:09:31] done +36: [23:09:31] done +36: [23:09:31] ------------------------------------- +36: [23:09:31] Testing Github2441: Add RDProps interface to Conformers. +36: [23:09:31] done +36: [23:09:31] ------------------------------------- +36: [23:09:31] Testing Issue2510: Pickle Confs as double. +36: [23:09:31] done +36: [23:09:31] ------------------------------------- +36: [23:09:31] Testing Github #2465: Negative atom-map numbers cause depickling to fail. +36: [23:09:31] done +36: [23:09:31] ------------------------------------- +36: [23:09:31] Testing loading pickled mols with conformers +36: [23:09:31] done +36: [23:09:31] ------------------------------------- +36: [23:09:31] Testing conformer reading/writing options +36: [23:09:31] done +36: [23:09:31] ------------------------------------- +36: [23:09:31] Testing property reading options +36: [23:09:31] done +36: [23:09:31] ------------------------------------- +36: [23:09:31] Testing property reading options +36: [23:09:31] done +36: [23:09:31] ------------------------------------- +36: [23:09:31] Testing boost::serialization integration +36: [23:09:31] done +36: [23:09:31] ------------------------------------- +36: [23:09:31] Testing github issue 6036 + 35/230 Test #36: graphmoltestPickler .................... Passed 0.60 sec test 47 Start 47: graphmolSGroupCatch 47: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolSGroupCatch 47: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol 47: Test timeout computed to be: 1500 -45: [02:22:46] Explicit valence for atom # 2 O, 3, is greater than permitted -45: [02:22:46] Explicit valence for atom # 2 O, 3, is greater than permitted -45: [02:22:46] non-ring atom 2 marked aromatic -45: [02:22:46] non-ring atom 2 marked aromatic -45: [02:22:46] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -45: [02:22:46] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -45: [02:22:46] Can't kekulize mol. Unkekulized atoms: 1 2 3 -45: [02:22:46] Can't kekulize mol. Unkekulized atoms: 1 2 3 -45: [02:22:46] Can't kekulize mol. Unkekulized atoms: 0 1 2 -45: [02:22:46] Can't kekulize mol. Unkekulized atoms: 0 1 2 -45: [02:22:46] Explicit valence for atom # 1 O, 3, is greater than permitted -45: [02:22:46] Explicit valence for atom # 4 F, 2, is greater than permitted -45: [02:22:46] Can't kekulize mol. Unkekulized atoms: 6 7 8 -45: [02:22:46] Explicit valence for atom # 1 C, 5, is greater than permitted -45: [02:22:46] WARNING: not removing hydrogen atom with dummy atom neighbors -45: [02:22:46] WARNING: not removing hydrogen atom with dummy atom neighbors -45: [02:22:46] WARNING: not removing hydrogen atom with wedged bond -45: [02:22:46] WARNING: not removing hydrogen atom without neighbors -45: [02:22:46] WARNING: not removing hydrogen atom without neighbors -45: [02:22:46] WARNING: not removing hydrogen atom without neighbors -45: [02:22:46] WARNING: not removing hydrogen atom without neighbors -45: [02:22:46] Unreasonable formal charge on atom # 0. -34: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 - 36/230 Test #43: testSGroup ............................. Passed 0.12 sec -test 48 - Start 48: graphmolAdjustQueryCatch - -48: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolAdjustQueryCatch -48: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol -48: Test timeout computed to be: 1500 -45: [02:22:46] +28: ......[23:09:31] Molecule does not have explicit Hs. Consider calling AddHs() +28: [23:09:31] +28: +28: **** +45: Randomness seeded to: 166525584 +45: [23:09:31] WARNING: not removing hydrogen atom without neighbors +45: [23:09:31] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +45: [23:09:31] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +45: [23:09:31] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +45: [23:09:31] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +45: [23:09:31] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +45: [23:09:31] Explicit valence for atom # 1 N, 5, is greater than permitted +45: [23:09:31] Explicit valence for atom # 1 N, 6, is greater than permitted +45: [23:09:31] Explicit valence for atom # 1 N, 5, is greater than permitted +45: [23:09:31] Explicit valence for atom # 1 N, 5, is greater than permitted +45: [23:09:31] Explicit valence for atom # 2 O, 3, is greater than permitted +45: [23:09:31] Explicit valence for atom # 2 O, 3, is greater than permitted +45: [23:09:31] non-ring atom 2 marked aromatic +45: [23:09:31] non-ring atom 2 marked aromatic +45: [23:09:31] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +45: [23:09:31] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +45: [23:09:31] Can't kekulize mol. Unkekulized atoms: 1 2 3 +45: [23:09:31] Can't kekulize mol. Unkekulized atoms: 1 2 3 +45: [23:09:31] Can't kekulize mol. Unkekulized atoms: 0 1 2 +45: [23:09:31] Can't kekulize mol. Unkekulized atoms: 0 1 2 +45: [23:09:31] Explicit valence for atom # 1 O, 3, is greater than permitted +45: [23:09:31] Explicit valence for atom # 4 F, 2, is greater than permitted +45: [23:09:31] Can't kekulize mol. Unkekulized atoms: 6 7 8 +45: [23:09:31] Explicit valence for atom # 1 C, 5, is greater than permitted +45: [23:09:31] WARNING: not removing hydrogen atom with dummy atom neighbors +45: [23:09:31] WARNING: not removing hydrogen atom with dummy atom neighbors +45: [23:09:31] WARNING: not removing hydrogen atom with wedged bond +45: [23:09:31] WARNING: not removing hydrogen atom without neighbors +45: [23:09:31] WARNING: not removing hydrogen atom without neighbors +45: [23:09:31] WARNING: not removing hydrogen atom without neighbors +45: [23:09:31] WARNING: not removing hydrogen atom without neighbors +45: [23:09:31] Unreasonable formal charge on atom # 0. +45: [23:09:31] 45: 45: **** 45: Pre-condition Violation @@ -18208,20 +18259,20 @@ 45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x0000AAAAB608A244 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x0000AAAAB60D624C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x0000AAAAB60D6C00 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x0000AAAAB60D7034 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x0000AAAAB60AA558 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x0000AAAAB60AAAA4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x0000AAAAB602D470 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0x0000FFFF9348229C in /lib/aarch64-linux-gnu/libc.so.6 +45: 3# 0x0000AAAAE600A244 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x0000AAAAE605624C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x0000AAAAE6056C00 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x0000AAAAE6057034 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x0000AAAAE602A558 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x0000AAAAE602AAA4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x0000AAAAE5FAD470 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0x0000FFFF8A32229C in /lib/aarch64-linux-gnu/libc.so.6 45: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -45: 12# 0x0000AAAAB602D530 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 12# 0x0000AAAAE5FAD530 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: ---------- 45: **** 45: -45: [02:22:46] +45: [23:09:31] 45: 45: **** 45: Pre-condition Violation @@ -18233,20 +18284,20 @@ 45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x0000AAAAB608A2B8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x0000AAAAB60D624C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x0000AAAAB60D6C00 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x0000AAAAB60D7034 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x0000AAAAB60AA558 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x0000AAAAB60AAAA4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x0000AAAAB602D470 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0x0000FFFF9348229C in /lib/aarch64-linux-gnu/libc.so.6 +45: 3# 0x0000AAAAE600A2B8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x0000AAAAE605624C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x0000AAAAE6056C00 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x0000AAAAE6057034 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x0000AAAAE602A558 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x0000AAAAE602AAA4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x0000AAAAE5FAD470 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0x0000FFFF8A32229C in /lib/aarch64-linux-gnu/libc.so.6 45: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -45: 12# 0x0000AAAAB602D530 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 12# 0x0000AAAAE5FAD530 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: ---------- 45: **** 45: -45: [02:22:46] +45: [23:09:31] 45: 45: **** 45: Pre-condition Violation @@ -18258,20 +18309,98 @@ 45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x0000AAAAB608A338 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x0000AAAAB60D624C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x0000AAAAB60D6C00 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x0000AAAAB60D7034 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x0000AAAAB60AA558 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x0000AAAAB60AAAA4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x0000AAAAB602D470 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0x0000FFFF9348229C in /lib/aarch64-linux-gnu/libc.so.6 +45: 3# 0x0000AAAAE600A338 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x0000AAAAE605624C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x0000AAAAE6056C00 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x0000AAAAE6057034 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x0000AAAAE602A558 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x0000AAAAE602AAA4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x0000AAAAE5FAD470 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0x0000FFFF8A32229C in /lib/aarch64-linux-gnu/libc.so.6 45: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -45: 12# 0x0000AAAAB602D530 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 12# 0x0000AAAAE5FAD530 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: ---------- 45: **** 45: -45: [02:22:46] +28: Invariant Violation +28: bad direction in linearSearch +28: Violation occurred on line 240 in file ./Code/Numerics/Optimizer/BFGSOpt.h +28: Failed Expression: status >= 0 +28: ---------- +28: Stacktrace: +28: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +28: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +28: 2# ForceFields::ForceField::minimize(unsigned int, std::vector >*, unsigned int, double, double) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitForceField.so.1 +28: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/ForceField/rdForceField.so +28: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +28: 5# 0x0000FFFF95AD15C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +28: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +28: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +28: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +28: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +28: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +28: 11# 0x0000FFFF935B4180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +28: 12# 0x0000FFFF935B4118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +28: 13# 0x0000FFFF935B40A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +28: 14# 0x0000FFFF935B4040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +28: 15# 0x0000FFFF935B3FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +28: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so +28: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so +28: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so +28: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so +28: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +28: 21# 0x0000FFFF95ACE19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +28: 22# _PyObject_MakeTpCall in /usr/bin/python3 +28: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 +28: 24# 0x00000000004C3D1C in /usr/bin/python3 +28: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 +28: 26# _PyObject_Call_Prepend in /usr/bin/python3 +28: 27# 0x000000000051FB4C in /usr/bin/python3 +28: 28# 0x000000000051B324 in /usr/bin/python3 +28: 29# _PyObject_MakeTpCall in /usr/bin/python3 +28: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 +28: 31# 0x00000000004C3D1C in /usr/bin/python3 +28: 32# _PyEval_EvalFrameDefault in /usr/bin/python3 +28: 33# _PyObject_Call_Prepend in /usr/bin/python3 +28: 34# 0x000000000052608C in /usr/bin/python3 +28: 35# _PyObject_MakeTpCall in /usr/bin/python3 +28: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 +28: 37# 0x00000000004C3D1C in /usr/bin/python3 +28: 38# _PyEval_EvalFrameDefault in /usr/bin/python3 +28: 39# _PyObject_Call_Prepend in /usr/bin/python3 +28: 40# 0x000000000052608C in /usr/bin/python3 +28: 41# _PyObject_MakeTpCall in /usr/bin/python3 +28: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 +28: 43# 0x00000000004C3D1C in /usr/bin/python3 +28: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 +28: 45# _PyObject_Call_Prepend in /usr/bin/python3 +28: 46# 0x000000000052608C in /usr/bin/python3 +28: 47# _PyObject_MakeTpCall in /usr/bin/python3 +28: 48# _PyEval_EvalFrameDefault in /usr/bin/python3 +28: 49# _PyObject_Call_Prepend in /usr/bin/python3 +28: 50# 0x000000000051FB4C in /usr/bin/python3 +28: 51# 0x000000000051B324 in /usr/bin/python3 +28: 52# _PyObject_MakeTpCall in /usr/bin/python3 +28: 53# _PyEval_EvalFrameDefault in /usr/bin/python3 +28: 54# PyEval_EvalCode in /usr/bin/python3 +28: 55# 0x0000000000595200 in /usr/bin/python3 +28: 56# 0x00000000006757AC in /usr/bin/python3 +28: 57# _PyRun_SimpleFileObject in /usr/bin/python3 +28: 58# _PyRun_AnyFileObject in /usr/bin/python3 +28: 59# Py_RunMain in /usr/bin/python3 +28: 60# Py_BytesMain in /usr/bin/python3 +28: 61# 0x0000FFFF962B229C in /lib/aarch64-linux-gnu/libc.so.6 +28: 62# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +28: 63# _start in /usr/bin/python3 +28: ---------- +28: **** +28: +30: ...... +30: ---------------------------------------------------------------------- +30: Ran 6 tests in 0.004s +30: +30: OK +45: [23:09:31] 45: 45: **** 45: Pre-condition Violation @@ -18283,20 +18412,20 @@ 45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x0000AAAAB608A400 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x0000AAAAB60D624C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x0000AAAAB60D6C00 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x0000AAAAB60D7034 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x0000AAAAB60AA558 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x0000AAAAB60AAAA4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x0000AAAAB602D470 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0x0000FFFF9348229C in /lib/aarch64-linux-gnu/libc.so.6 +45: 3# 0x0000AAAAE600A400 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x0000AAAAE605624C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x0000AAAAE6056C00 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x0000AAAAE6057034 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x0000AAAAE602A558 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x0000AAAAE602AAA4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x0000AAAAE5FAD470 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0x0000FFFF8A32229C in /lib/aarch64-linux-gnu/libc.so.6 45: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -45: 12# 0x0000AAAAB602D530 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 12# 0x0000AAAAE5FAD530 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: ---------- 45: **** 45: -45: [02:22:46] +45: [23:09:31] 45: 45: **** 45: Pre-condition Violation @@ -18308,20 +18437,20 @@ 45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x0000AAAAB608A478 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x0000AAAAB60D624C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x0000AAAAB60D6C00 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x0000AAAAB60D7034 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x0000AAAAB60AA558 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x0000AAAAB60AAAA4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x0000AAAAB602D470 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0x0000FFFF9348229C in /lib/aarch64-linux-gnu/libc.so.6 +45: 3# 0x0000AAAAE600A478 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x0000AAAAE605624C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x0000AAAAE6056C00 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x0000AAAAE6057034 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x0000AAAAE602A558 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x0000AAAAE602AAA4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x0000AAAAE5FAD470 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0x0000FFFF8A32229C in /lib/aarch64-linux-gnu/libc.so.6 45: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -45: 12# 0x0000AAAAB602D530 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 12# 0x0000AAAAE5FAD530 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: ---------- 45: **** 45: -45: [02:22:46] +45: [23:09:31] 45: 45: **** 45: Pre-condition Violation @@ -18333,20 +18462,20 @@ 45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x0000AAAAB608A4FC in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x0000AAAAB60D624C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x0000AAAAB60D6C00 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x0000AAAAB60D7034 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x0000AAAAB60AA558 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x0000AAAAB60AAAA4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x0000AAAAB602D470 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0x0000FFFF9348229C in /lib/aarch64-linux-gnu/libc.so.6 +45: 3# 0x0000AAAAE600A4FC in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x0000AAAAE605624C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x0000AAAAE6056C00 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x0000AAAAE6057034 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x0000AAAAE602A558 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x0000AAAAE602AAA4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x0000AAAAE5FAD470 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0x0000FFFF8A32229C in /lib/aarch64-linux-gnu/libc.so.6 45: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -45: 12# 0x0000AAAAB602D530 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 12# 0x0000AAAAE5FAD530 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: ---------- 45: **** 45: -45: [02:22:46] +45: [23:09:31] 45: 45: **** 45: Pre-condition Violation @@ -18358,20 +18487,20 @@ 45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x0000AAAAB608AC10 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x0000AAAAB60D624C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x0000AAAAB60D6C00 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x0000AAAAB60D7034 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x0000AAAAB60AA558 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x0000AAAAB60AAAA4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x0000AAAAB602D470 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0x0000FFFF9348229C in /lib/aarch64-linux-gnu/libc.so.6 +45: 3# 0x0000AAAAE600AC10 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x0000AAAAE605624C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x0000AAAAE6056C00 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x0000AAAAE6057034 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x0000AAAAE602A558 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x0000AAAAE602AAA4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x0000AAAAE5FAD470 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0x0000FFFF8A32229C in /lib/aarch64-linux-gnu/libc.so.6 45: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -45: 12# 0x0000AAAAB602D530 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 12# 0x0000AAAAE5FAD530 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: ---------- 45: **** 45: -45: [02:22:46] +45: [23:09:31] 45: 45: **** 45: Pre-condition Violation @@ -18383,20 +18512,20 @@ 45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x0000AAAAB608A62C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x0000AAAAB60D624C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x0000AAAAB60D6C00 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x0000AAAAB60D7034 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x0000AAAAB60AA558 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x0000AAAAB60AAAA4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x0000AAAAB602D470 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0x0000FFFF9348229C in /lib/aarch64-linux-gnu/libc.so.6 +45: 3# 0x0000AAAAE600A62C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x0000AAAAE605624C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x0000AAAAE6056C00 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x0000AAAAE6057034 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x0000AAAAE602A558 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x0000AAAAE602AAA4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x0000AAAAE5FAD470 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0x0000FFFF8A32229C in /lib/aarch64-linux-gnu/libc.so.6 45: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -45: 12# 0x0000AAAAB602D530 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 12# 0x0000AAAAE5FAD530 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: ---------- 45: **** 45: -45: [02:22:46] +45: [23:09:31] 45: 45: **** 45: Pre-condition Violation @@ -18408,20 +18537,20 @@ 45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x0000AAAAB608A6B0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x0000AAAAB60D624C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x0000AAAAB60D6C00 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x0000AAAAB60D7034 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x0000AAAAB60AA558 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x0000AAAAB60AAAA4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x0000AAAAB602D470 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0x0000FFFF9348229C in /lib/aarch64-linux-gnu/libc.so.6 +45: 3# 0x0000AAAAE600A6B0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x0000AAAAE605624C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x0000AAAAE6056C00 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x0000AAAAE6057034 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x0000AAAAE602A558 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x0000AAAAE602AAA4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x0000AAAAE5FAD470 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0x0000FFFF8A32229C in /lib/aarch64-linux-gnu/libc.so.6 45: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -45: 12# 0x0000AAAAB602D530 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 12# 0x0000AAAAE5FAD530 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: ---------- 45: **** 45: -45: [02:22:46] +45: [23:09:31] 45: 45: **** 45: Pre-condition Violation @@ -18433,20 +18562,20 @@ 45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x0000AAAAB608ABF4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x0000AAAAB60D624C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x0000AAAAB60D6C00 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x0000AAAAB60D7034 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x0000AAAAB60AA558 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x0000AAAAB60AAAA4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x0000AAAAB602D470 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0x0000FFFF9348229C in /lib/aarch64-linux-gnu/libc.so.6 +45: 3# 0x0000AAAAE600ABF4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x0000AAAAE605624C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x0000AAAAE6056C00 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x0000AAAAE6057034 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x0000AAAAE602A558 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x0000AAAAE602AAA4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x0000AAAAE5FAD470 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0x0000FFFF8A32229C in /lib/aarch64-linux-gnu/libc.so.6 45: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -45: 12# 0x0000AAAAB602D530 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 12# 0x0000AAAAE5FAD530 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: ---------- 45: **** 45: -45: [02:22:46] +45: [23:09:31] 45: 45: **** 45: Pre-condition Violation @@ -18458,20 +18587,20 @@ 45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x0000AAAAB608A8A0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x0000AAAAB60D624C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x0000AAAAB60D6C00 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x0000AAAAB60D7034 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x0000AAAAB60AA558 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x0000AAAAB60AAAA4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x0000AAAAB602D470 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0x0000FFFF9348229C in /lib/aarch64-linux-gnu/libc.so.6 +45: 3# 0x0000AAAAE600A8A0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x0000AAAAE605624C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x0000AAAAE6056C00 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x0000AAAAE6057034 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x0000AAAAE602A558 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x0000AAAAE602AAA4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x0000AAAAE5FAD470 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0x0000FFFF8A32229C in /lib/aarch64-linux-gnu/libc.so.6 45: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -45: 12# 0x0000AAAAB602D530 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 12# 0x0000AAAAE5FAD530 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: ---------- 45: **** 45: -45: [02:22:46] +45: [23:09:31] 45: 45: **** 45: Pre-condition Violation @@ -18483,24 +18612,24 @@ 45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x0000AAAAB608ABD4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x0000AAAAB60D624C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x0000AAAAB60D6C00 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x0000AAAAB60D7034 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x0000AAAAB60AA558 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x0000AAAAB60AAAA4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x0000AAAAB602D470 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0x0000FFFF9348229C in /lib/aarch64-linux-gnu/libc.so.6 +45: 3# 0x0000AAAAE600ABD4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x0000AAAAE605624C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x0000AAAAE6056C00 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x0000AAAAE6057034 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x0000AAAAE602A558 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x0000AAAAE602AAA4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x0000AAAAE5FAD470 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0x0000FFFF8A32229C in /lib/aarch64-linux-gnu/libc.so.6 45: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -45: 12# 0x0000AAAAB602D530 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 12# 0x0000AAAAE5FAD530 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: ---------- 45: **** 45: -45: [02:22:46] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -45: [02:22:46] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -45: [02:22:46] WARNING: not removing hydrogen atom without neighbors -45: [02:22:46] Explicit valence for atom # 1 F greater than permitted -45: [02:22:46] +45: [23:09:31] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +45: [23:09:31] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +45: [23:09:31] WARNING: not removing hydrogen atom without neighbors +45: [23:09:31] Explicit valence for atom # 1 F greater than permitted +45: [23:09:31] 45: 45: **** 45: Pre-condition Violation @@ -18512,20 +18641,20 @@ 45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 2# RDKit::Atom::setQuery(Queries::Query*) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x0000AAAAB603A5EC in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x0000AAAAB60D624C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x0000AAAAB60D6C00 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x0000AAAAB60D7034 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x0000AAAAB60AA558 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x0000AAAAB60AAAA4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x0000AAAAB602D470 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0x0000FFFF9348229C in /lib/aarch64-linux-gnu/libc.so.6 +45: 3# 0x0000AAAAE5FBA5EC in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x0000AAAAE605624C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x0000AAAAE6056C00 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x0000AAAAE6057034 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x0000AAAAE602A558 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x0000AAAAE602AAA4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x0000AAAAE5FAD470 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0x0000FFFF8A32229C in /lib/aarch64-linux-gnu/libc.so.6 45: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -45: 12# 0x0000AAAAB602D530 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 12# 0x0000AAAAE5FAD530 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: ---------- 45: **** 45: -45: [02:22:46] +45: [23:09:31] 45: 45: **** 45: Pre-condition Violation @@ -18537,20 +18666,20 @@ 45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 2# RDKit::Atom::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x0000AAAAB603A678 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x0000AAAAB60D624C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x0000AAAAB60D6C00 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x0000AAAAB60D7034 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x0000AAAAB60AA558 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x0000AAAAB60AAAA4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x0000AAAAB602D470 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0x0000FFFF9348229C in /lib/aarch64-linux-gnu/libc.so.6 +45: 3# 0x0000AAAAE5FBA678 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x0000AAAAE605624C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x0000AAAAE6056C00 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x0000AAAAE6057034 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x0000AAAAE602A558 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x0000AAAAE602AAA4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x0000AAAAE5FAD470 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0x0000FFFF8A32229C in /lib/aarch64-linux-gnu/libc.so.6 45: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -45: 12# 0x0000AAAAB602D530 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 12# 0x0000AAAAE5FAD530 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: ---------- 45: **** 45: -45: [02:22:46] +45: [23:09:31] 45: 45: **** 45: Pre-condition Violation @@ -18562,20 +18691,20 @@ 45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 2# RDKit::Bond::setQuery(Queries::Query*) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x0000AAAAB603A23C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x0000AAAAB60D624C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x0000AAAAB60D6C00 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x0000AAAAB60D7034 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x0000AAAAB60AA558 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x0000AAAAB60AAAA4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x0000AAAAB602D470 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0x0000FFFF9348229C in /lib/aarch64-linux-gnu/libc.so.6 +45: 3# 0x0000AAAAE5FBA23C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x0000AAAAE605624C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x0000AAAAE6056C00 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x0000AAAAE6057034 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x0000AAAAE602A558 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x0000AAAAE602AAA4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x0000AAAAE5FAD470 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0x0000FFFF8A32229C in /lib/aarch64-linux-gnu/libc.so.6 45: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -45: 12# 0x0000AAAAB602D530 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 12# 0x0000AAAAE5FAD530 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: ---------- 45: **** 45: -45: [02:22:46] +45: [23:09:31] 45: 45: **** 45: Pre-condition Violation @@ -18587,491 +18716,301 @@ 45: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 45: 2# RDKit::Bond::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -45: 3# 0x0000AAAAB603A2C8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 4# 0x0000AAAAB60D624C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 5# 0x0000AAAAB60D6C00 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 6# 0x0000AAAAB60D7034 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 7# 0x0000AAAAB60AA558 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 8# 0x0000AAAAB60AAAA4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 9# 0x0000AAAAB602D470 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -45: 10# 0x0000FFFF9348229C in /lib/aarch64-linux-gnu/libc.so.6 +45: 3# 0x0000AAAAE5FBA2C8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 4# 0x0000AAAAE605624C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 5# 0x0000AAAAE6056C00 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 6# 0x0000AAAAE6057034 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 7# 0x0000AAAAE602A558 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 8# 0x0000AAAAE602AAA4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 9# 0x0000AAAAE5FAD470 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 10# 0x0000FFFF8A32229C in /lib/aarch64-linux-gnu/libc.so.6 45: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -45: 12# 0x0000AAAAB602D530 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +45: 12# 0x0000AAAAE5FAD530 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 45: ---------- 45: **** 45: -45: [02:22:46] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -45: [02:22:46] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -45: [02:22:46] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -45: [02:22:46] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -45: [02:22:46] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -45: [02:22:46] Unusual charge on atom 0 number of radical electrons set to zero -45: [02:22:46] Unusual charge on atom 0 number of radical electrons set to zero -45: [02:22:46] Unusual charge on atom 0 number of radical electrons set to zero -45: [02:22:46] non-ring atom 0 marked aromatic -45: [02:22:46] non-ring atom 0 marked aromatic -45: [02:22:46] Explicit valence for atom # 1 C, 5, is greater than permitted -45: [02:22:46] Explicit valence for atom # 9 C, 5, is greater than permitted -45: [02:22:46] Explicit valence for atom # 3 N, 4, is greater than permitted -45: [02:22:46] Explicit valence for atom # 15 C, 5, is greater than permitted -45: [02:22:46] Explicit valence for atom # 11 C, 5, is greater than permitted -45: [02:22:46] Explicit valence for atom # 9 C, 5, is greater than permitted -45: [02:22:46] Explicit valence for atom # 9 C, 5, is greater than permitted -45: [02:22:46] Explicit valence for atom # 9 C, 6, is greater than permitted -45: [02:22:46] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -45: [02:22:46] Can't kekulize mol. Unkekulized atoms: 7 -45: [02:22:46] Can't kekulize mol. Unkekulized atoms: 3 -45: [02:22:46] Can't kekulize mol. Unkekulized atoms: 3 7 -45: [02:22:46] Can't kekulize mol. Unkekulized atoms: 3 7 -47: Randomness seeded to: 4174075583 +45: [23:09:31] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +45: [23:09:31] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: Randomness seeded to: 504588134 +46: =============================================================================== +46: All tests passed (62 assertions in 6 test cases) +46: + 36/230 Test #46: graphmolOrganometallicsCatch ........... Passed 0.14 sec +test 48 + Start 48: graphmolAdjustQueryCatch + +48: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/graphmolAdjustQueryCatch +48: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol +48: Test timeout computed to be: 1500 +45: [23:09:31] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +45: [23:09:31] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +45: [23:09:31] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +45: [23:09:31] Unusual charge on atom 0 number of radical electrons set to zero +45: [23:09:31] Unusual charge on atom 0 number of radical electrons set to zero +45: [23:09:31] Unusual charge on atom 0 number of radical electrons set to zero +45: [23:09:31] non-ring atom 0 marked aromatic +45: [23:09:31] non-ring atom 0 marked aromatic +45: [23:09:31] Explicit valence for atom # 1 C, 5, is greater than permitted +45: [23:09:31] Explicit valence for atom # 9 C, 5, is greater than permitted +45: [23:09:31] Explicit valence for atom # 3 N, 4, is greater than permitted +45: [23:09:31] Explicit valence for atom # 15 C, 5, is greater than permitted +45: [23:09:31] Explicit valence for atom # 11 C, 5, is greater than permitted +45: [23:09:31] Explicit valence for atom # 9 C, 5, is greater than permitted +45: [23:09:31] Explicit valence for atom # 9 C, 5, is greater than permitted +45: [23:09:31] Explicit valence for atom # 9 C, 6, is greater than permitted +45: [23:09:31] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +45: [23:09:31] Can't kekulize mol. Unkekulized atoms: 7 +45: [23:09:31] Can't kekulize mol. Unkekulized atoms: 3 +45: [23:09:31] Can't kekulize mol. Unkekulized atoms: 3 7 +47: Randomness seeded to: 1024387169 47: =============================================================================== 47: All tests passed (136 assertions in 8 test cases) 47: -39: [02:22:46] sorting (hanoi sort) vectors -45: [02:22:46] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. - 37/230 Test #47: graphmolSGroupCatch .................... Passed 0.05 sec + 37/230 Test #47: graphmolSGroupCatch .................... Passed 0.10 sec test 49 Start 49: chiralityTestsCatch 49: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/chiralityTestsCatch 49: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol 49: Test timeout computed to be: 1500 -34: [02:22:46] non-ring atom 0 marked aromatic -34: [02:22:46] non-ring atom 0 marked aromatic -45: [02:22:46] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -34: [02:22:46] Conflicting single bond directions around double bond at index 17. -34: [02:22:46] BondStereo set to STEREONONE and single bond directions set to NONE. -46: Randomness seeded to: 640888932 -46: =============================================================================== -46: All tests passed (62 assertions in 6 test cases) -46: -48: Randomness seeded to: 1162540863 +45: [23:09:31] Can't kekulize mol. Unkekulized atoms: 3 7 +45: [23:09:31] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +45: [23:09:31] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +39: [23:09:31] sorting (hanoi sort) vectors +48: Randomness seeded to: 3344851710 48: =============================================================================== 48: All tests passed (281 assertions in 10 test cases) 48: - 38/230 Test #46: graphmolOrganometallicsCatch ........... Passed 0.10 sec - 39/230 Test #48: graphmolAdjustQueryCatch ............... Passed 0.07 sec + 38/230 Test #48: graphmolAdjustQueryCatch ............... Passed 0.09 sec test 50 Start 50: canonTestsCatch 50: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/canonTestsCatch 50: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol 50: Test timeout computed to be: 1500 +28: ... +28: ---------------------------------------------------------------------- +28: Ran 12 tests in 0.653s +28: +28: OK +49: Randomness seeded to: 412069245 +49: [23:09:31] unable to set wavy bonds for double bonds: 3 +45: [23:09:31] Explicit valence for atom # 1 O, 3, is greater than permitted +45: [23:09:31] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +45: [23:09:31] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +45: [23:09:31] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +45: [23:09:31] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +45: [23:09:31] Invalid value for molAttachPoint: 4 on atom 1. Not expanding this atttachment point. +45: [23:09:31] Invalid value for _fromAttachPoint: -1 on atom 0. Not collapsing this atom +45: [23:09:31] Invalid value for _fromAttachPoint: 4 on atom 0. Not collapsing this atom +45: [23:09:31] non-ring atom 0 marked aromatic +45: [23:09:31] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +45: [23:09:31] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +49: [23:09:31] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +49: [23:09:31] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry + 39/230 Test #30: pyDistGeom ............................. Passed 1.04 sec test 51 Start 51: moliteratorTestsCatch 51: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/moliteratorTestsCatch 51: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol 51: Test timeout computed to be: 1500 -34: starting ring finding -34: done -34: starting ring finding -34: done -34: starting ring finding -34: done -34: C/C=N/c1ccc(cc1)c1cc2cc(c1)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)C)c1ccc(cc1)C=Nc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)/N=C/C)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(c3ccc(C=Nc4ccc(c5cc6c7ccc(N=Cc8ccc(c9cc(c%10ccc(C=Nc%11ccc2cc%11)cc%10)cc(c9)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)N=Cc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)C)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(c9ccc(N=Cc%10ccc(c%11cc(c%12ccc(C=Nc%13ccc(c(c6)c5)cc%13)cc%12)cc(c%11)c5ccc(cc5)C)cc%10)cc9)cc(c2)c2ccc(cc2)/N=C/C)c2ccc(cc2)/N=C/C)cc8)cc7)cc4)cc3)cc(c1)c1ccc(cc1)C -34: starting sanitization -34: done -34: starting sanitization -34: done -34: starting ring finding -34: done -34: starting ring finding -34: done -34: smiles: CC[C@]1(C(=O)c([nH])n)CC[C@](C)(O)CC1 -45: [02:22:46] Explicit valence for atom # 1 O, 3, is greater than permitted -45: [02:22:46] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -45: [02:22:46] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -45: [02:22:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -45: [02:22:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -49: Randomness seeded to: 3606654300 -49: [02:22:46] unable to set wavy bonds for double bonds: 3 -45: [02:22:46] Invalid value for molAttachPoint: 4 on atom 1. Not expanding this atttachment point. -45: [02:22:46] Invalid value for _fromAttachPoint: -1 on atom 0. Not collapsing this atom -45: [02:22:46] Invalid value for _fromAttachPoint: 4 on atom 0. Not collapsing this atom -45: [02:22:46] non-ring atom 0 marked aromatic -45: [02:22:46] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -45: [02:22:46] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -34: [02:22:46] WARNING: not removing hydrogen atom with dummy atom neighbors -34: ------------------------------- -34: [02:22:46] Explicit valence for atom # 0 N, 4, is greater than permitted -51: Randomness seeded to: 3393096659 +45: [23:09:31] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +45: [23:09:31] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +49: [23:09:31] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. +49: [23:09:31] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. +45: [23:09:31] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +45: [23:09:31] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +45: [23:09:31] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +49: [23:09:31] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored +51: Randomness seeded to: 657519871 51: =============================================================================== 51: All tests passed (14 assertions in 4 test cases) 51: -34: [02:22:46] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -34: [02:22:46] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -34: [02:22:46] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -34: [02:22:46] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged - 40/230 Test #51: moliteratorTestsCatch .................. Passed 0.03 sec + 40/230 Test #51: moliteratorTestsCatch .................. Passed 0.07 sec test 52 Start 52: queryTestsCatch 52: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/queryTestsCatch 52: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol 52: Test timeout computed to be: 1500 -34: [02:22:46] WARNING: not removing hydrogen atom with dummy atom neighbors -45: [02:22:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -49: [02:22:46] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -49: [02:22:46] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -49: [02:22:46] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. -49: [02:22:46] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. -52: Randomness seeded to: 1913550843 -52: =============================================================================== -52: All tests passed (10 assertions in 1 test case) -52: -45: [02:22:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 41/230 Test #52: queryTestsCatch ........................ Passed 0.02 sec +49: =============================================================================== +49: All tests passed (2267 assertions in 79 test cases) +49: + 41/230 Test #49: chiralityTestsCatch .................... Passed 0.29 sec test 53 Start 53: molbundleTestsCatch 53: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/molbundleTestsCatch 53: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol 53: Test timeout computed to be: 1500 -49: [02:22:46] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored -49: =============================================================================== -49: All tests passed (2267 assertions in 79 test cases) -49: - 42/230 Test #49: chiralityTestsCatch .................... Passed 0.12 sec +45: [23:09:31] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +45: [23:09:31] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +45: [23:09:31] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +45: [23:09:31] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +45: [23:09:31] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +52: Randomness seeded to: 1708418695 +52: =============================================================================== +52: All tests passed (10 assertions in 1 test case) +52: + 42/230 Test #52: queryTestsCatch ........................ Passed 0.06 sec test 54 Start 54: pickleTestsCatch 54: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/pickleTestsCatch 54: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol 54: Test timeout computed to be: 1500 -45: [02:22:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -45: [02:22:46] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -45: [02:22:46] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -53: Randomness seeded to: 1723496723 +45: [23:09:31] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +53: Randomness seeded to: 2751849052 53: =============================================================================== 53: All tests passed (6 assertions in 1 test case) 53: - 43/230 Test #53: molbundleTestsCatch .................... Passed 0.04 sec + 43/230 Test #53: molbundleTestsCatch .................... Passed 0.07 sec test 55 Start 55: tableTestsCatch 55: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/tableTestsCatch 55: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol 55: Test timeout computed to be: 1500 -45: [02:22:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -28: ......[02:22:46] Molecule does not have explicit Hs. Consider calling AddHs() -28: [02:22:46] -28: -28: **** -45: [02:22:46] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -45: [02:22:46] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -45: [02:22:46] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -45: [02:22:46] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -54: Randomness seeded to: 2193031197 -54: =============================================================================== -54: All tests passed (45 assertions in 4 test cases) -54: -45: [02:22:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 44/230 Test #54: pickleTestsCatch ....................... Passed 0.05 sec + 44/230 Test #28: pyForceFieldConstraints ................ Passed 1.79 sec test 56 Start 56: molopsTestsCatch 56: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/molopsTestsCatch 56: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol 56: Test timeout computed to be: 1500 -55: Randomness seeded to: 4269648223 -55: =============================================================================== -55: All tests passed (7 assertions in 2 test cases) -55: - 45/230 Test #55: tableTestsCatch ........................ Passed 0.04 sec +54: Randomness seeded to: 3692332455 +54: =============================================================================== +54: All tests passed (45 assertions in 4 test cases) +54: + 45/230 Test #54: pickleTestsCatch ....................... Passed 0.10 sec test 57 Start 57: smiTest1 57: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTest1 57: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 57: Test timeout computed to be: 1500 -56: Randomness seeded to: 1697878986 +56: Randomness seeded to: 1726443573 56: =============================================================================== 56: All tests passed (72 assertions in 4 test cases) 56: - 46/230 Test #56: molopsTestsCatch ....................... Passed 0.04 sec + 46/230 Test #56: molopsTestsCatch ....................... Passed 0.06 sec test 58 Start 58: smiTest2 58: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTest2 58: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 58: Test timeout computed to be: 1500 -57: [02:22:46] WARNING: not removing hydrogen atom without neighbors -57: [02:22:46] WARNING: not removing hydrogen atom without neighbors -57: [02:22:46] WARNING: not removing hydrogen atom without neighbors -57: [02:22:46] WARNING: not removing hydrogen atom without neighbors -57: [02:22:46] WARNING: not removing hydrogen atom without neighbors -57: [02:22:46] WARNING: not removing hydrogen atom without neighbors -57: [02:22:46] WARNING: not removing hydrogen atom without neighbors -57: [02:22:46] WARNING: not removing hydrogen atom without neighbors -57: [02:22:46] WARNING: not removing hydrogen atom without neighbors -57: [02:22:46] WARNING: not removing hydrogen atom without neighbors -58: [02:22:46] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' -58: [02:22:46] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -58: [02:22:46] SMILES Parse Error: syntax error while parsing: - -58: [02:22:46] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' -58: [02:22:46] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' -58: [02:22:46] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' -58: [02:22:46] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -58: [02:22:46] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' -58: [02:22:46] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' -58: [02:22:46] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' -58: [02:22:46] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' -58: [02:22:46] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' -58: [02:22:46] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' -58: [02:22:46] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' -58: [02:22:46] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' - 47/230 Test #58: smiTest2 ............................... Passed 0.02 sec +58: [23:09:31] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' +58: [23:09:31] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +58: [23:09:31] SMILES Parse Error: syntax error while parsing: - +58: [23:09:31] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' +58: [23:09:31] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' +58: [23:09:31] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' +58: [23:09:31] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +58: [23:09:31] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' +58: [23:09:31] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' +58: [23:09:31] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' +58: [23:09:31] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' +58: [23:09:31] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' +58: [23:09:31] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' +58: [23:09:31] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' +58: [23:09:31] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' + 47/230 Test #58: smiTest2 ............................... Passed 0.03 sec test 59 Start 59: cxsmilesTest 59: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/cxsmilesTest 59: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 59: Test timeout computed to be: 1500 -57: [02:22:46] WARNING: not removing hydrogen atom without neighbors -57: [02:22:46] Invalid chiral specification on atom 0 -57: [02:22:46] Invalid chiral specification on atom 0 -57: [02:22:46] Invalid chiral specification on atom 0 -57: [02:22:46] Invalid chiral specification on atom 0 -57: [02:22:46] Invalid chiral specification on atom 0 -28: Invariant Violation -28: bad direction in linearSearch -28: Violation occurred on line 240 in file ./Code/Numerics/Optimizer/BFGSOpt.h -28: Failed Expression: status >= 0 -28: ---------- -28: Stacktrace: -28: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -28: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -28: 2# ForceFields::ForceField::minimize(unsigned int, std::vector >*, unsigned int, double, double) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitForceField.so.1 -28: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/ForceField/rdForceField.so -28: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -28: 5# 0x0000FFFF8C6915C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -28: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -28: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -28: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -28: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -28: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -28: 11# 0x0000FFFF8A174180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -28: 12# 0x0000FFFF8A174118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -28: 13# 0x0000FFFF8A1740A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -28: 14# 0x0000FFFF8A174040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -28: 15# 0x0000FFFF8A173FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -28: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so -28: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so -28: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so -28: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so -28: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -28: 21# 0x0000FFFF8C68E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -28: 22# _PyObject_MakeTpCall in /usr/bin/python3 -28: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 -28: 24# 0x00000000004C3D1C in /usr/bin/python3 -28: 25# _PyEval_EvalFrameDefault in /usr/bin/python3 -28: 26# _PyObject_Call_Prepend in /usr/bin/python3 -28: 27# 0x000000000051FB4C in /usr/bin/python3 -28: 28# 0x000000000051B324 in /usr/bin/python3 -28: 29# _PyObject_MakeTpCall in /usr/bin/python3 -28: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 -28: 31# 0x00000000004C3D1C in /usr/bin/python3 -28: 32# _PyEval_EvalFrameDefault in /usr/bin/python3 -28: 33# _PyObject_Call_Prepend in /usr/bin/python3 -28: 34# 0x000000000052608C in /usr/bin/python3 -28: 35# _PyObject_MakeTpCall in /usr/bin/python3 -28: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 -28: 37# 0x00000000004C3D1C in /usr/bin/python3 -28: 38# _PyEval_EvalFrameDefault in /usr/bin/python3 -28: 39# _PyObject_Call_Prepend in /usr/bin/python3 -28: 40# 0x000000000052608C in /usr/bin/python3 -28: 41# _PyObject_MakeTpCall in /usr/bin/python3 -28: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 -28: 43# 0x00000000004C3D1C in /usr/bin/python3 -28: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 -28: 45# _PyObject_Call_Prepend in /usr/bin/python3 -28: 46# 0x000000000052608C in /usr/bin/python3 -28: 47# _PyObject_MakeTpCall in /usr/bin/python3 -28: 48# _PyEval_EvalFrameDefault in /usr/bin/python3 -28: 49# _PyObject_Call_Prepend in /usr/bin/python3 -28: 50# 0x000000000051FB4C in /usr/bin/python3 -28: 51# 0x000000000051B324 in /usr/bin/python3 -28: 52# _PyObject_MakeTpCall in /usr/bin/python3 -28: 53# _PyEval_EvalFrameDefault in /usr/bin/python3 -28: 54# PyEval_EvalCode in /usr/bin/python3 -28: 55# 0x0000000000595200 in /usr/bin/python3 -28: 56# 0x00000000006757AC in /usr/bin/python3 -28: 57# _PyRun_SimpleFileObject in /usr/bin/python3 -28: 58# _PyRun_AnyFileObject in /usr/bin/python3 -28: 59# Py_RunMain in /usr/bin/python3 -28: 60# Py_BytesMain in /usr/bin/python3 -28: 61# 0x0000FFFF8CE7229C in /lib/aarch64-linux-gnu/libc.so.6 -28: 62# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -28: 63# _start in /usr/bin/python3 -28: ---------- -28: **** -28: -57: [02:22:46] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' -57: [02:22:46] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' -45: [02:22:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -45: [02:22:46] Explicit valence for atom # 0 Al, 6, is greater than permitted -45: [02:22:46] Explicit valence for atom # 0 Al, 6, is greater than permitted -45: [02:22:46] Explicit valence for atom # 1 Si, 6, is greater than permitted -45: [02:22:46] Explicit valence for atom # 1 Si, 6, is greater than permitted -45: [02:22:46] Explicit valence for atom # 0 P, 6, is greater than permitted -45: [02:22:46] Explicit valence for atom # 0 P, 6, is greater than permitted -45: [02:22:46] Explicit valence for atom # 0 P, 7, is greater than permitted -45: [02:22:46] Explicit valence for atom # 0 P, 7, is greater than permitted -45: [02:22:46] Explicit valence for atom # 1 As, 6, is greater than permitted -45: [02:22:46] Explicit valence for atom # 1 As, 6, is greater than permitted -45: [02:22:46] Explicit valence for atom # 1 As, 7, is greater than permitted -45: [02:22:46] Explicit valence for atom # 1 As, 7, is greater than permitted -45: [02:22:46] Explicit valence for atom # 0 Sb, 6, is greater than permitted -45: [02:22:46] Explicit valence for atom # 0 Sb, 6, is greater than permitted -45: [02:22:46] Explicit valence for atom # 0 Sb, 7, is greater than permitted -45: [02:22:46] Explicit valence for atom # 0 Sb, 7, is greater than permitted -45: [02:22:46] Explicit valence for atom # 1 Bi, 6, is greater than permitted -45: [02:22:46] Explicit valence for atom # 1 Bi, 6, is greater than permitted -45: [02:22:46] Explicit valence for atom # 1 Bi, 8, is greater than permitted -45: [02:22:46] Explicit valence for atom # 1 Bi, 8, is greater than permitted +45: [23:09:31] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +45: [23:09:31] Explicit valence for atom # 0 Al, 6, is greater than permitted +45: [23:09:31] Explicit valence for atom # 0 Al, 6, is greater than permitted +45: [23:09:31] Explicit valence for atom # 1 Si, 6, is greater than permitted +45: [23:09:31] Explicit valence for atom # 1 Si, 6, is greater than permitted +45: [23:09:31] Explicit valence for atom # 0 P, 6, is greater than permitted +45: [23:09:31] Explicit valence for atom # 0 P, 6, is greater than permitted +45: [23:09:31] Explicit valence for atom # 0 P, 7, is greater than permitted +45: [23:09:31] Explicit valence for atom # 0 P, 7, is greater than permitted +45: [23:09:31] Explicit valence for atom # 1 As, 6, is greater than permitted +45: [23:09:31] Explicit valence for atom # 1 As, 6, is greater than permitted +45: [23:09:31] Explicit valence for atom # 1 As, 7, is greater than permitted +45: [23:09:31] Explicit valence for atom # 1 As, 7, is greater than permitted +45: [23:09:31] Explicit valence for atom # 0 Sb, 6, is greater than permitted +45: [23:09:31] Explicit valence for atom # 0 Sb, 6, is greater than permitted +45: [23:09:31] Explicit valence for atom # 0 Sb, 7, is greater than permitted +45: [23:09:31] Explicit valence for atom # 0 Sb, 7, is greater than permitted +45: [23:09:31] Explicit valence for atom # 1 Bi, 6, is greater than permitted +45: [23:09:31] Explicit valence for atom # 1 Bi, 6, is greater than permitted +45: [23:09:31] Explicit valence for atom # 1 Bi, 8, is greater than permitted +45: [23:09:31] Explicit valence for atom # 1 Bi, 8, is greater than permitted 45: =============================================================================== 45: All tests passed (4464 assertions in 106 test cases) 45: - 48/230 Test #45: graphmolTestsCatch ..................... Passed 0.41 sec + 48/230 Test #45: graphmolTestsCatch ..................... Passed 0.71 sec test 60 Start 60: smaTest1 60: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smaTest1 60: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 60: Test timeout computed to be: 1500 -57: --C1CCC2(CC1)CCCCC2CCC1CCCC1 -34: [02:22:46] Maximum BFS search size exceeded. -34: This is likely due to a highly symmetric fused ring system. -57: smi: ClC1CCCCC1 -57: smi: ClC1CCCCC1 -57: smi: ClC1CCCCC1Br -57: smi: c1ccccc1 -57: smi: c1ccncc1 -57: smi: c1cc[nH]c1 -57: smi: c1cc[nH]c1 -57: smi: c1cc[pH]c1 -57: CbC(aC)aC -57: CaC(bC)aC -57: CbC(bC)aC -57: O.C -57: C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O -57: [02:22:46] SMILES Parse Error: syntax error while parsing: c%()ccccc%() -57: [02:22:46] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' -57: [02:22:46] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) -57: [02:22:46] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' -57: [02:22:46] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' -28: ... -28: ---------------------------------------------------------------------- -28: Ran 12 tests in 0.595s -28: -28: OK -57: [02:22:46] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' -57: [02:22:46] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -57: [02:22:46] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -57: [02:22:46] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -57: [02:22:46] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -57: [02:22:46] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -57: [02:22:46] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -57: [02:22:46] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -57: [02:22:46] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -57: [02:22:46] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -57: [02:22:46] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -57: [02:22:46] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -57: [02:22:46] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -57: C=c1s/c2n(c1=O)CCCCCCC\N=2 -57: C1=C\C/C=C2C3=C\C/C=C\C=C/C/3C\2\C=C/1 -57: [02:22:46] SMILES Parse Error: extra close parentheses while parsing: C) -57: [02:22:46] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' - 49/230 Test #57: smiTest1 ............................... Passed 0.21 sec +57: [23:09:31] WARNING: not removing hydrogen atom without neighbors +57: [23:09:31] WARNING: not removing hydrogen atom without neighbors +57: [23:09:31] WARNING: not removing hydrogen atom without neighbors +57: [23:09:31] WARNING: not removing hydrogen atom without neighbors +57: [23:09:31] WARNING: not removing hydrogen atom without neighbors +57: [23:09:31] WARNING: not removing hydrogen atom without neighbors +57: [23:09:31] WARNING: not removing hydrogen atom without neighbors +57: [23:09:31] WARNING: not removing hydrogen atom without neighbors +57: [23:09:31] WARNING: not removing hydrogen atom without neighbors +57: [23:09:31] WARNING: not removing hydrogen atom without neighbors +57: [23:09:31] WARNING: not removing hydrogen atom without neighbors +57: [23:09:31] Invalid chiral specification on atom 0 +57: [23:09:31] Invalid chiral specification on atom 0 +57: [23:09:31] Invalid chiral specification on atom 0 +57: [23:09:31] Invalid chiral specification on atom 0 +57: [23:09:31] Invalid chiral specification on atom 0 +57: [23:09:32] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' +57: [23:09:32] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' +55: Randomness seeded to: 693325060 +55: =============================================================================== +55: All tests passed (7 assertions in 2 test cases) +55: + 49/230 Test #55: tableTestsCatch ........................ Passed 0.32 sec test 61 Start 61: smiTestCatch 61: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 61: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 61: Test timeout computed to be: 1500 -60: [02:22:46] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC -60: [02:22:46] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' -60: [02:22:46] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON -60: [02:22:46] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' -60: [02:22:46] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -60: [02:22:46] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged - 50/230 Test #60: smaTest1 ............................... Passed 0.14 sec +34: [23:09:32] Maximum BFS search size exceeded. +34: This is likely due to a highly symmetric fused ring system. +61: Randomness seeded to: 1878268545 +61: [23:09:32] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +61: [23:09:32] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +61: [23:09:32] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' +61: [23:09:32] SMARTS Parse Error: unclosed ring for input: 'C1C' +61: [23:09:32] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +61: [23:09:32] SMARTS Parse Error: syntax error while parsing: C)foo +61: [23:09:32] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' +61: [23:09:32] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| +61: [23:09:32] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' +60: [23:09:32] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC +60: [23:09:32] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' +60: [23:09:32] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON +60: [23:09:32] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' +61: [23:09:32] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' +60: [23:09:32] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +60: [23:09:32] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged + 50/230 Test #60: smaTest1 ............................... Passed 0.29 sec test 62 Start 62: nontetrahedralCatch 62: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/nontetrahedralCatch 62: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 62: Test timeout computed to be: 1500 -61: Randomness seeded to: 2890880370 -61: [02:22:46] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -61: [02:22:46] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -61: [02:22:46] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' -61: [02:22:46] SMARTS Parse Error: unclosed ring for input: 'C1C' -61: [02:22:46] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -61: [02:22:46] SMARTS Parse Error: syntax error while parsing: C)foo -61: [02:22:46] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' -61: [02:22:46] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| -61: [02:22:46] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' -61: [02:22:46] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' -62: Randomness seeded to: 3320029298 -62: [02:22:46] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -62: [02:22:46] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -62: [02:22:46] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -62: [02:22:46] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -62: [02:22:46] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -62: [02:22:46] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -62: [02:22:46] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -62: [02:22:46] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -62: [02:22:46] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. -62: =============================================================================== -62: All tests passed (308 assertions in 9 test cases) -62: - 51/230 Test #62: nontetrahedralCatch .................... Passed 0.08 sec -test 63 - Start 63: v2smiTestCatch - -63: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/v2smiTestCatch -63: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse -63: Test timeout computed to be: 1500 -61: [02:22:46] w block attempts to set wedging on bond 0 more than once. -61: [02:22:46] improperly formatted w block -61: [02:22:46] atom 3 is not associated with bond 1(1-2) in w block -63: Randomness seeded to: 1946616711 -63: =============================================================================== -63: All tests passed (14 assertions in 2 test cases) -63: - 52/230 Test #63: v2smiTestCatch ......................... Passed 0.04 sec -test 64 - Start 64: testDepictor - -64: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/testDepictor -64: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Depictor -64: Test timeout computed to be: 1500 -61: [02:22:46] SMARTS Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' -61: [02:22:46] SMILES Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' -61: [02:22:46] SMARTS Parse Error: syntax error while parsing: C1C)foo -61: [02:22:46] SMARTS Parse Error: Failed parsing SMARTS 'C1C)foo' for input: 'C1C)foo' -61: [02:22:46] SMILES Parse Error: extra close parentheses while parsing: C1C)foo -61: [02:22:46] SMILES Parse Error: Failed parsing SMILES 'C1C)foo' for input: 'C1C)foo' -61: =============================================================================== -61: All tests passed (1570 assertions in 66 test cases) -61: - 53/230 Test #61: smiTestCatch ........................... Passed 0.19 sec -test 65 - Start 65: depictorCatch - -65: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/depictorCatch -65: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Depictor -65: Test timeout computed to be: 1500 - 54/230 Test #28: pyForceFieldConstraints ................ Passed 1.10 sec -test 66 - Start 66: pyDepictor - -66: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Depictor/Wrap/testDepictor.py" -66: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/Wrap -66: Test timeout computed to be: 1500 -59: Randomness seeded to: 1240540966 +57: --C1CCC2(CC1)CCCCC2CCC1CCCC1 +59: Randomness seeded to: 1555400423 59: Test 59: 59: ShortAtropisomerNoCoords.cxsmi @@ -19132,16 +19071,18 @@ 59: 59: BMS-986142_atrop5.cxsmi 59: -59: [02:22:46] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [02:22:46] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [02:22:46] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [02:22:46] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [02:22:46] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [02:22:46] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [02:22:46] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [02:22:46] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [02:22:46] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [02:22:46] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [23:09:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [23:09:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [23:09:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [23:09:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [23:09:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [23:09:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [23:09:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [23:09:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [23:09:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [23:09:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +62: Randomness seeded to: 3872379402 +62: [23:09:32] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 59: Test 59: 59: BMS-986142_atrop6.cxsmi @@ -19150,20 +19091,110 @@ 59: 59: BMS-986142_atropBad1.cxsmi 59: -59: [02:22:46] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -59: [02:22:46] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -59: [02:22:46] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -59: [02:22:46] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -59: [02:22:46] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +59: [23:09:32] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +59: [23:09:32] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +57: smi: ClC1CCCCC1 +57: smi: ClC1CCCCC1 +57: smi: ClC1CCCCC1Br +57: smi: c1ccccc1 +57: smi: c1ccncc1 +57: smi: c1cc[nH]c1 +57: smi: c1cc[nH]c1 +57: smi: c1cc[pH]c1 +57: CbC(aC)aC +57: CaC(bC)aC +57: CbC(bC)aC +57: O.C +59: [23:09:32] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +59: [23:09:32] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +59: [23:09:32] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 59: Test 59: 59: BMS-986142_atropBad2.cxsmi 59: -59: [02:22:46] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -59: [02:22:46] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -59: [02:22:46] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -59: [02:22:46] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -59: [02:22:46] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +59: [23:09:32] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +59: [23:09:32] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +61: [23:09:32] w block attempts to set wedging on bond 0 more than once. +61: [23:09:32] improperly formatted w block +62: [23:09:32] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +57: C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O +57: [23:09:32] SMILES Parse Error: syntax error while parsing: c%()ccccc%() +57: [23:09:32] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' +57: [23:09:32] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) +57: [23:09:32] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' +57: [23:09:32] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' +57: [23:09:32] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' +61: [23:09:32] atom 3 is not associated with bond 1(1-2) in w block +59: [23:09:32] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +59: [23:09:32] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +59: [23:09:32] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +62: [23:09:32] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +62: [23:09:32] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +62: [23:09:32] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +62: [23:09:32] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +57: [23:09:32] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +57: [23:09:32] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +57: [23:09:32] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +57: [23:09:32] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +57: [23:09:32] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +57: [23:09:32] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +57: [23:09:32] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +57: [23:09:32] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +57: [23:09:32] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +57: [23:09:32] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +57: [23:09:32] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +57: [23:09:32] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +57: C=c1s/c2n(c1=O)CCCCCCC\N=2 +57: C1=C\C/C=C2C3=C\C/C=C\C=C/C/3C\2\C=C/1 +57: [23:09:32] SMILES Parse Error: extra close parentheses while parsing: C) +57: [23:09:32] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' +61: [23:09:32] SMARTS Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' +61: [23:09:32] SMILES Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' +61: [23:09:32] SMARTS Parse Error: syntax error while parsing: C1C)foo +61: [23:09:32] SMARTS Parse Error: Failed parsing SMARTS 'C1C)foo' for input: 'C1C)foo' +61: [23:09:32] SMILES Parse Error: extra close parentheses while parsing: C1C)foo +61: [23:09:32] SMILES Parse Error: Failed parsing SMILES 'C1C)foo' for input: 'C1C)foo' + 51/230 Test #57: smiTest1 ............................... Passed 0.52 sec +test 63 + Start 63: v2smiTestCatch + +63: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/v2smiTestCatch +63: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse +63: Test timeout computed to be: 1500 +62: [23:09:32] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +62: [23:09:32] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +62: [23:09:32] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. +61: =============================================================================== +61: All tests passed (1570 assertions in 66 test cases) +61: + 52/230 Test #61: smiTestCatch ........................... Passed 0.28 sec +test 64 + Start 64: testDepictor + +64: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/testDepictor +64: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Depictor +64: Test timeout computed to be: 1500 +62: =============================================================================== +62: All tests passed (308 assertions in 9 test cases) +62: + 53/230 Test #62: nontetrahedralCatch .................... Passed 0.18 sec +test 65 + Start 65: depictorCatch + +65: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/depictorCatch +65: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Depictor +65: Test timeout computed to be: 1500 +63: Randomness seeded to: 2791977040 +63: =============================================================================== +63: All tests passed (14 assertions in 2 test cases) +63: + 54/230 Test #63: v2smiTestCatch ......................... Passed 0.06 sec +test 66 + Start 66: pyDepictor + +66: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Depictor/Wrap/testDepictor.py" +66: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/Wrap +66: Test timeout computed to be: 1500 59: Test 59: 59: JDQ443_3d.cxsmi @@ -19188,29 +19219,11 @@ 59: 59: JDQ443_atropBad1.cxsmi 59: -59: [02:22:46] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -59: [02:22:46] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -59: [02:22:46] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -59: [02:22:46] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -59: [02:22:46] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -34: [02:22:46] Maximum BFS search size exceeded. -34: This is likely due to a highly symmetric fused ring system. -65: Randomness seeded to: 2186079848 -65: =============================================================================== -65: All tests passed (577 assertions in 17 test cases) -65: - 55/230 Test #65: depictorCatch .......................... Passed 0.22 sec -test 67 - Start 67: testMrvToMol - -67: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -67: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse -67: Test timeout computed to be: 1500 -34: F/C=C/Cl -34: [H]/C(F)=C(/[H])Cl -34: F/C=C/Cl -34: F/C=C/Cl -34: C/C(F)=C(/C)Cl +59: [23:09:32] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +59: [23:09:32] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +59: [23:09:32] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +59: [23:09:32] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +59: [23:09:32] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 59: Test 59: 59: RP-6306_atrop1.cxsmi @@ -19231,25 +19244,16 @@ 59: 59: RP-6306_atrop5.cxsmi 59: -59: [02:22:46] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [02:22:46] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [02:22:46] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [02:22:46] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -34: [02:22:47] ----------------------- -34: Testing isRingFused -59: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -59: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored - 56/230 Test #34: graphmolMolOpsTest ..................... Passed 1.20 sec -test 68 - Start 68: fileParsersTest1 - -68: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -68: Test timeout computed to be: 1500 +59: [23:09:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [23:09:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [23:09:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [23:09:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [23:09:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [23:09:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [23:09:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [23:09:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [23:09:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [23:09:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 59: Test 59: 59: RP-6306_atrop6.cxsmi @@ -19258,21 +19262,20 @@ 59: 59: RP-6306_atropBad1.cxsmi 59: -59: [02:22:47] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -59: [02:22:47] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -59: [02:22:47] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -59: [02:22:47] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -59: [02:22:47] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +59: [23:09:32] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +59: [23:09:32] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +59: [23:09:32] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +59: [23:09:32] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +59: [23:09:32] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 59: Test 59: 59: RP-6306_atropBad2.cxsmi 59: -59: [02:22:47] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -59: [02:22:47] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -59: [02:22:47] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -59: [02:22:47] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -59: [02:22:47] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -64: [02:22:47] Warning: stereochemistry around double bond may be incorrect in depiction. +59: [23:09:32] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +59: [23:09:32] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +59: [23:09:32] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +59: [23:09:32] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +59: [23:09:32] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 59: Test 59: 59: RP-6306_3d.cxsmi @@ -19297,38 +19300,74 @@ 59: 59: Sotorasib_atrop5.cxsmi 59: -59: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -59: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -59: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -59: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -59: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -59: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -59: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -59: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -59: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -59: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +59: [23:09:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +59: [23:09:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +59: [23:09:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +59: [23:09:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +59: [23:09:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +59: [23:09:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +59: [23:09:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +59: [23:09:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +59: [23:09:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +59: [23:09:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored 59: Test 59: 59: Sotorasib_atropBad1.cxsmi 59: -59: [02:22:47] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -68: *************************************** -68: *************************************** -68: [02:22:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: [02:22:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -59: [02:22:47] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -59: [02:22:47] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -59: [02:22:47] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -59: [02:22:47] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +59: [23:09:32] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +59: [23:09:32] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +59: [23:09:32] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +59: [23:09:32] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +59: [23:09:32] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 59: Test 59: 59: Sotorasib_atropBad2.cxsmi 59: -59: [02:22:47] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -59: [02:22:47] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -59: [02:22:47] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -59: [02:22:47] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -59: [02:22:47] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +59: [23:09:32] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +59: [23:09:32] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +65: Randomness seeded to: 939138632 +65: =============================================================================== +65: All tests passed (577 assertions in 17 test cases) +65: + 55/230 Test #65: depictorCatch .......................... Passed 0.28 sec +test 67 + Start 67: testMrvToMol + +67: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +67: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse +67: Test timeout computed to be: 1500 +59: [23:09:32] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +59: [23:09:32] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +59: [23:09:32] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +59: Test +59: +59: Sotorasib_3d.cxsmi +59: +59: Test +59: +59: ZM374979_atrop1.cxsmi +59: +59: Test +59: +59: ZM374979_atrop2.cxsmi +59: +59: Test +59: +59: ZM374979_atrop3.cxsmi +59: +59: Test +59: +59: ZM374979_atrop4.cxsmi +59: +59: Test +59: +59: ZM374979_atropBad1.cxsmi +59: +59: [23:09:32] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +59: [23:09:32] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +59: [23:09:32] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +59: [23:09:32] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +59: [23:09:32] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 67: Using new chirality perception 67: Test 67: @@ -19366,220 +19405,79 @@ 67: 67: ProblemShort.mol 67: -67: [02:22:47] For a MultipleSgroup expansion, the matching orphaned bond was not found +67: [23:09:32] For a MultipleSgroup expansion, the matching orphaned bond was not found 67: The multiple sgroup will be ignored - 57/230 Test #64: testDepictor ........................... Passed 0.42 sec -test 69 - Start 69: testAtropisomers - -69: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testAtropisomers -69: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -69: Test timeout computed to be: 1500 -68: [02:22:47] bond with order 0 found on line 7. This is not part of the MDL specification. -69: [02:22:47] ---- Running with POSIX locale ----- -59: Test -59: -59: Sotorasib_3d.cxsmi -59: -59: Test -59: -59: ZM374979_atrop1.cxsmi -59: 59: Test 59: -59: ZM374979_atrop2.cxsmi +59: Mrtx1719_3d.cxsmi 59: 59: Test 59: -59: ZM374979_atrop3.cxsmi +59: Mrtx1719_atrop1.cxsmi 59: 59: Test 59: -59: ZM374979_atrop4.cxsmi +59: Mrtx1719_atrop2.cxsmi 59: 59: Test 59: -59: ZM374979_atropBad1.cxsmi +59: Mrtx1719_atrop3.cxsmi 59: -59: [02:22:47] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -68: [02:22:47] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -68: [02:22:47] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -68: [02:22:47] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -59: [02:22:47] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -59: [02:22:47] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -68: generating smiles -68: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 -68: converting back -59: [02:22:47] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -59: [02:22:47] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -69: [02:22:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [02:22:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: check isomorphism -69: [02:22:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [02:22:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [02:22:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [02:22:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [02:22:47] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -69: [02:22:47] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -69: [02:22:47] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -69: [02:22:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [02:22:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 59: Test 59: -59: Mrtx1719_3d.cxsmi +59: Mrtx1719_atrop4.cxsmi 59: 59: Test 59: -59: Mrtx1719_atrop1.cxsmi +59: Mrtx1719_atropBad1.cxsmi 59: -59: Test -59: -59: Mrtx1719_atrop2.cxsmi -59: -59: Test -59: -59: Mrtx1719_atrop3.cxsmi -59: -59: Test -59: -59: Mrtx1719_atrop4.cxsmi -59: -59: Test -59: -59: Mrtx1719_atropBad1.cxsmi -59: -59: [02:22:47] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -59: [02:22:47] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -59: [02:22:47] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -59: [02:22:47] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -59: [02:22:47] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -69: [02:22:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [02:22:47] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -69: [02:22:47] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -69: [02:22:47] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -69: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [02:22:47] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -69: [02:22:47] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -69: [02:22:47] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -69: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [02:22:47] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -69: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [02:22:47] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -69: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [02:22:47] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -69: [02:22:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [02:22:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [02:22:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -66: ..............[02:22:47] SMILES Parse Error: syntax error while parsing: invalidsmiles -66: [02:22:47] SMILES Parse Error: Failed parsing SMILES 'invalidsmiles' for input: 'invalidsmiles' -69: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [02:22:47] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -69: [02:22:47] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -69: [02:22:47] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -69: [02:22:47] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -69: [02:22:47] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -69: [02:22:47] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -69: [02:22:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [02:22:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [02:22:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [02:22:47] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -69: [02:22:47] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -69: [02:22:47] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -69: [02:22:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [02:22:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [02:22:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -66: ..... -66: ---------------------------------------------------------------------- -66: Ran 19 tests in 0.368s -66: -66: OK -69: [02:22:47] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -69: [02:22:47] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -69: [02:22:47] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 - 58/230 Test #66: pyDepictor ............................. Passed 0.74 sec -test 70 - Start 70: testSquiggleDoubleBonds - -70: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testSquiggleDoubleBonds -70: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -70: Test timeout computed to be: 1500 -70: Randomness seeded to: 3250414477 -70: =============================================================================== -70: All tests passed (15 assertions in 3 test cases) -70: - 59/230 Test #70: testSquiggleDoubleBonds ................ Passed 0.04 sec -test 71 - Start 71: testMolSupplier +59: [23:09:32] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +59: [23:09:32] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +59: [23:09:32] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +59: [23:09:32] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +59: [23:09:32] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +34: [23:09:33] Maximum BFS search size exceeded. +34: This is likely due to a highly symmetric fused ring system. +34: F/C=C/Cl +34: [H]/C(F)=C(/[H])Cl +34: F/C=C/Cl +34: F/C=C/Cl +34: C/C(F)=C(/C)Cl +34: [23:09:33] ----------------------- +34: Testing isRingFused + 56/230 Test #34: graphmolMolOpsTest ..................... Passed 2.47 sec +test 68 + Start 68: fileParsersTest1 -71: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -71: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -71: Test timeout computed to be: 1500 -71: [02:22:47] -71: ----------------------------------------- -71: [02:22:47] -71: -71: **** -71: Invariant Violation -71: bad prop value -71: Violation occurred on line 155 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp -71: Failed Expression: nSwaps < 2 -71: ---------- -71: Stacktrace: -71: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -71: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -71: 2# 0x0000FFFFA8DB79D8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -71: 3# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -71: 4# 0x0000AAAAB4E1E17C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -71: 5# 0x0000AAAAB4E12528 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -71: 6# 0x0000AAAAB4DE0874 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -71: 7# 0x0000FFFFA83C229C in /lib/aarch64-linux-gnu/libc.so.6 -71: 8# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -71: 9# 0x0000AAAAB4DE21B0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -71: ---------- -71: **** -71: -69: Atropisomers- 1 hits 3 misses -69: Final results: -69: Found atropisomers in TestMultInSDF.sdf - 1 hits 4 misses - 60/230 Test #69: testAtropisomers ....................... Passed 0.54 sec -test 72 - Start 72: testGeneralFileReader +68: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +68: Test timeout computed to be: 1500 +64: [23:09:33] Warning: stereochemistry around double bond may be incorrect in depiction. +68: *************************************** +68: *************************************** +68: [23:09:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: [23:09:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: [23:09:33] bond with order 0 found on line 7. This is not part of the MDL specification. +68: [23:09:33] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +68: [23:09:33] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +68: [23:09:33] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +68: generating smiles +68: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 +68: converting back +68: check isomorphism + 57/230 Test #64: testDepictor ........................... Passed 1.06 sec +test 69 + Start 69: testAtropisomers -72: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader -72: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -72: Test timeout computed to be: 1500 -72: [02:22:47] -72: ----------------------------------------- -72: [02:22:47] Finished: testDetermineFormat() -72: [02:22:47] ----------------------------------------- -72: -72: [02:22:47] -72: ----------------------------------------- +69: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testAtropisomers +69: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +69: Test timeout computed to be: 1500 +69: [23:09:33] ---- Running with POSIX locale ----- +69: [23:09:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [23:09:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [23:09:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [23:09:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [23:09:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 67: Test 67: 67: badWedgeError.sdf @@ -19892,13 +19790,9 @@ 67: 67: MulticenterSgroup.mrv 67: -67: [02:22:47] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -67: [02:22:47] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -72: [02:22:47] Finished: testSdf() -72: [02:22:47] ----------------------------------------- -72: -72: [02:22:47] -72: ----------------------------------------- +67: [23:09:33] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +67: [23:09:33] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +69: [23:09:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 67: Test 67: 67: GenericSgroup.mrv @@ -19931,7 +19825,7 @@ 67: 67: MarvinBadMissingMolID.mrv 67: -67: [02:22:47] +67: [23:09:33] 67: 67: **** 67: Test Assert @@ -19942,12 +19836,12 @@ 67: Stacktrace: 67: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 67: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -67: 2# 0x0000AAAAE3C4A99C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -67: 3# 0x0000AAAAE3C55A20 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -67: 4# 0x0000AAAAE3C44658 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -67: 5# 0x0000FFFFB65D229C in /lib/aarch64-linux-gnu/libc.so.6 +67: 2# 0x0000AAAAB6F0A99C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +67: 3# 0x0000AAAAB6F15A20 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +67: 4# 0x0000AAAAB6F04658 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +67: 5# 0x0000FFFF944D229C in /lib/aarch64-linux-gnu/libc.so.6 67: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -67: 7# 0x0000AAAAE3C448B0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +67: 7# 0x0000AAAAB6F048B0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol 67: ---------- 67: **** 67: @@ -19988,6 +19882,12 @@ 67: MarvinBadMissingBondOrder.mrv 67: 67: bond must have one of: order, queryType, or convention in MRV File +69: [23:09:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [23:09:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [23:09:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [23:09:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [23:09:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [23:09:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 67: Test 67: 67: MarvinBadMissingSruMolID.mrv @@ -20052,11 +19952,13 @@ 67: MarvinBadSupAttachOrder.mrv 67: 67: Order for an AttachmentPoint definition must be an integer in MRV file -72: [02:22:47] Finished: testSmi() -72: [02:22:47] ----------------------------------------- -72: -72: [02:22:47] -72: ----------------------------------------- +69: [23:09:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [23:09:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [23:09:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [23:09:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [23:09:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [23:09:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [23:09:33] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 67: Test 67: 67: MarvinBadSupAttachAtom.mrv @@ -20082,183 +19984,50 @@ 67: MarvinBadSupMissingAttachOrder.mrv 67: 67: Expected atom, order and bond, for an AttachmentPoint definition in MRV file -71: [02:22:47] Finished: testMolSup() -71: [02:22:47] ----------------------------------------- -71: -71: [02:22:47] ----------------------------------------- -71: [02:22:47] Finished: testRandMolSup() -71: [02:22:47] ----------------------------------------- -71: -71: [02:22:47] ----------------------------------------- -27: Checking against /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -71: [02:22:47] Finished: testSmilesSup() -71: [02:22:47] ----------------------------------------- -71: -71: [02:22:47] ----------------------------------------- -71: [02:22:47] ------------------------------------------------------ -71: [02:22:47] SMILES Parse Error: syntax error while parsing: fail -71: [02:22:47] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -71: [02:22:47] ERROR: Smiles parse error on line 3 -71: [02:22:47] ERROR: Cannot create molecule from : 'fail' -71: [02:22:47] ------------------------------------------------------ -71: [02:22:47] ------------------------------------------------------ -71: [02:22:47] >>> This may result in an infinite loop. It should finish almost immediately: -71: [02:22:47] <<< done. -71: [02:22:47] Finished: testSmilesSupFromText() -71: [02:22:47] ----------------------------------------- -71: -71: [02:22:47] ----------------------------------------- -71: [02:22:47] Finished: testSmilesWriter() -71: [02:22:47] ----------------------------------------- -71: -71: [02:22:47] ----------------------------------------- -71: [02:22:47] Finished: testSDWriter() -71: [02:22:47] ----------------------------------------- -71: -71: [02:22:47] ----------------------------------------- -71: [02:22:47] Finished: testSDSupplierEnding() -71: [02:22:47] ----------------------------------------- -71: -71: [02:22:47] ----------------------------------------- -72: [02:22:47] Finished: testMae() -72: [02:22:47] ----------------------------------------- -72: -72: [02:22:47] -72: ----------------------------------------- -71: [02:22:47] Finished: testSuppliersEmptyFile() -71: [02:22:47] ----------------------------------------- -71: -71: [02:22:47] ----------------------------------------- -71: [02:22:47] Finished: testCisTrans() -71: [02:22:47] ----------------------------------------- -71: -71: [02:22:47] ----------------------------------------- -72: [02:22:47] Finished: testTdt() -72: [02:22:47] ----------------------------------------- -72: - 61/230 Test #72: testGeneralFileReader .................. Passed 0.17 sec -test 73 - Start 73: testMultithreadedMolSupplier - -73: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier -73: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -73: Test timeout computed to be: 1500 -71: [02:22:47] Finished: testStereoRound() -71: [02:22:47] ----------------------------------------- -71: -71: [02:22:47] ----------------------------------------- -71: [02:22:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [02:22:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [02:22:47] Finished: testIssue226() -71: [02:22:47] ----------------------------------------- -71: -71: [02:22:47] ----------------------------------------- -71: [02:22:47] Finished: testTDTSupplier1() -71: [02:22:47] ----------------------------------------- -71: -71: [02:22:47] ----------------------------------------- -71: [02:22:47] Finished: testTDTSupplier2() -71: [02:22:47] ----------------------------------------- -71: -71: [02:22:47] ----------------------------------------- -71: [02:22:47] Finished: testTDTSupplier3() -71: [02:22:47] ----------------------------------------- -71: -71: [02:22:47] ----------------------------------------- -71: [02:22:47] Finished: testSDSupplierFromText() -71: [02:22:47] ----------------------------------------- -71: -71: [02:22:47] ----------------------------------------- -71: [02:22:47] ERROR: Problems encountered parsing data fields -71: [02:22:47] ERROR: moving to the beginning of the next molecule -71: [02:22:47] ERROR: Problems encountered parsing data fields -71: [02:22:47] ERROR: moving to the beginning of the next molecule -71: [02:22:47] Spurious data before the first property will be ignored -71: [02:22:47] Property will be truncated after the first blank line -71: [02:22:47] Property will be truncated after the first blank line -71: [02:22:47] Property will be truncated after the first blank line -71: [02:22:47] Finished: testSDSupplierStrLax1() -71: [02:22:47] ----------------------------------------- -71: -71: [02:22:47] ----------------------------------------- -71: [02:22:47] ERROR: Problems encountered parsing data fields -71: [02:22:47] ERROR: moving to the beginning of the next molecule -71: [02:22:47] Property will be truncated after the first blank line -71: [02:22:47] Finished: testSDSupplierStrLax2() -71: [02:22:47] ----------------------------------------- -71: -71: [02:22:47] ----------------------------------------- -71: [02:22:47] ERROR: Problems encountered parsing data fields -71: [02:22:47] ERROR: moving to the beginning of the next molecule -71: [02:22:47] ERROR: Problems encountered parsing data fields -71: [02:22:47] ERROR: moving to the beginning of the next molecule -71: [02:22:47] Spurious data before the first property will be ignored -71: [02:22:47] Property will be truncated after the first blank line -71: [02:22:47] Property will be truncated after the first blank line -71: [02:22:47] Property will be truncated after the first blank line -71: [02:22:47] Finished: testSDSupplierFromTextStrLax1() -71: [02:22:47] ----------------------------------------- -71: -71: [02:22:47] ----------------------------------------- -71: [02:22:47] ERROR: Problems encountered parsing data fields -71: [02:22:47] ERROR: moving to the beginning of the next molecule -71: [02:22:47] Property will be truncated after the first blank line -71: [02:22:47] Finished: testSDSupplierFromTextStrLax2() -71: [02:22:47] ----------------------------------------- -71: -71: [02:22:47] ----------------------------------------- -71: [02:22:47] Finished: testIssue265() -71: [02:22:47] ----------------------------------------- -71: -71: [02:22:47] ----------------------------------------- -71: [02:22:47] ERROR: End of data field name not found -71: [02:22:47] ERROR: moving to the beginning of the next molecule -71: [02:22:47] Explicit valence for atom # 0 F, 2, is greater than permitted -71: [02:22:47] ERROR: Could not sanitize molecule ending on line 16 -71: [02:22:47] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted -71: [02:22:47] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 -71: [02:22:47] ERROR: moving to the beginning of the next molecule -71: [02:22:47] ERROR: Bond line too short: 'M END' on line 18 -71: [02:22:47] ERROR: moving to the beginning of the next molecule -71: [02:22:47] Finished: testSDErrorHandling() -71: [02:22:47] ----------------------------------------- -71: -71: [02:22:47] ----------------------------------------- -71: [02:22:47] Finished: testIssue381() -71: [02:22:47] ----------------------------------------- -71: -71: [02:22:47] ----------------------------------------- -71: [02:22:47] Finished: testSetStreamIndices() -71: [02:22:47] ----------------------------------------- -71: -71: [02:22:47] ----------------------------------------- -71: [02:22:47] Finished: testMixIterAndRandom() -71: [02:22:47] ----------------------------------------- -71: -71: [02:22:47] ----------------------------------------- -71: build: -71: [02:22:47] Finished: testRemoveHs() -71: [02:22:47] ----------------------------------------- -71: -71: [02:22:47] ----------------------------------------- -73: [02:22:47] -73: ----------------------------------------- -71: [02:22:47] Finished: testGetItemText() -71: [02:22:47] ----------------------------------------- -71: -71: [02:22:47] ----------------------------------------- -71: [02:22:47] Finished: testForwardSDSupplier() -71: [02:22:47] ----------------------------------------- -71: -71: [02:22:47] ----------------------------------------- -71: [02:22:47] Finished: testMissingCRSDSupplier() -71: [02:22:47] ----------------------------------------- -71: -71: [02:22:47] ----------------------------------------- -71: [02:22:47] Finished: testIssue3482695() -71: [02:22:47] ----------------------------------------- -71: -71: [02:22:47] ----------------------------------------- +69: [23:09:33] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +69: [23:09:33] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +69: [23:09:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [23:09:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [23:09:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [23:09:33] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +69: [23:09:33] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +69: [23:09:33] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +69: [23:09:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [23:09:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [23:09:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [23:09:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [23:09:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [23:09:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [23:09:33] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +69: [23:09:33] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +69: [23:09:33] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +69: [23:09:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [23:09:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [23:09:33] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +69: [23:09:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [23:09:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [23:09:33] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +69: [23:09:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [23:09:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [23:09:33] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +69: [23:09:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [23:09:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [23:09:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [23:09:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [23:09:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [23:09:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [23:09:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [23:09:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [23:09:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [23:09:33] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +69: [23:09:33] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +69: [23:09:33] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +69: [23:09:33] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +69: [23:09:33] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +69: [23:09:33] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +69: [23:09:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [23:09:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [23:09:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 67: Test 67: 67: marvin03.mrv @@ -20323,31 +20092,17 @@ 67: 67: BMS-986142_atrop5.mrv 67: -67: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -67: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [02:22:47] ERROR: Cannot convert 'foo' to unsigned int on line 557 -71: [02:22:47] ERROR: moving to the beginning of the next molecule -71: [02:22:47] Finished: testIssue3525673() -71: [02:22:47] ----------------------------------------- -71: -71: [02:22:47] ----------------------------------------- -71: [02:22:47] Finished: testBlankLinesInProps() -71: [02:22:47] ----------------------------------------- -71: -71: [02:22:47] ----------------------------------------- -71: [02:22:47] Finished: testSkipLines() -71: [02:22:47] ----------------------------------------- -71: -71: [02:22:47] ----------------------------------------- -71: [02:22:47] Finished: testGitHub23() -71: [02:22:47] ----------------------------------------- -71: -71: [02:22:47] ----------------------------------------- -71: [02:22:47] Finished: testGitHub88() -71: [02:22:47] ----------------------------------------- -71: -71: [02:22:47] ----------------------------------------- -27: All 191 tests passed +67: [23:09:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +67: [23:09:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [23:09:33] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +69: [23:09:33] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +69: [23:09:33] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +69: [23:09:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [23:09:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [23:09:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [23:09:33] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +69: [23:09:33] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +69: [23:09:33] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 67: Test 67: 67: BMS-986142_atrop6.mrv @@ -20360,114 +20115,13 @@ 67: 67: BMS-986142_atrop8.mrv 67: -67: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -67: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +67: [23:09:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +67: [23:09:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 67: Test 67: 67: BMS-986142_atropBad2.mrv 67: -67: [02:22:47] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -71: [02:22:47] Finished: testGitHub2285() -71: [02:22:47] ----------------------------------------- -71: -71: [02:22:47] ----------------------------------------- -71: [02:22:47] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -71: [02:22:47] ERROR: Smiles parse error on line 1 -71: [02:22:47] ERROR: Cannot create molecule from : 'c1ccccc' -71: [02:22:47] SMILES Parse Error: extra open parentheses for input: 'C(C' -71: [02:22:47] ERROR: Smiles parse error on line 3 -71: [02:22:47] ERROR: Cannot create molecule from : 'C(C' -71: [02:22:47] Explicit valence for atom # 1 C, 5, is greater than permitted -71: [02:22:47] ERROR: Could not sanitize molecule on line 5 -71: [02:22:47] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -71: [02:22:47] Explicit valence for atom # 1 F, 2, is greater than permitted -71: [02:22:47] ERROR: Could not sanitize molecule ending on line 21 -71: [02:22:47] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -71: [02:22:47] Explicit valence for atom # 1 F, 2, is greater than permitted -71: [02:22:47] ERROR: Could not sanitize molecule ending on line 21 -71: [02:22:47] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -71: [02:22:47] Explicit valence for atom # 1 F, 2, is greater than permitted -71: [02:22:47] ERROR: Could not sanitize molecule ending on line 21 -71: [02:22:47] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -71: [02:22:47] ERROR: Atom line too short: ' -9.6' on line 28 -71: [02:22:47] ERROR: moving to the beginning of the next molecule -71: [02:22:47] Explicit valence for atom # 1 F, 2, is greater than permitted -71: [02:22:47] ERROR: Could not sanitize molecule ending on line 21 -71: [02:22:47] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -71: [02:22:47] ERROR: Atom line too short: ' -9.6' on line 28 -71: [02:22:47] ERROR: moving to the beginning of the next molecule -71: [02:22:47] Finished: testGitHub2479() -71: [02:22:47] ----------------------------------------- -71: -71: [02:22:47] ----------------------------------------- -71: [02:22:47] -71: -71: **** -71: Invariant Violation -71: bad chiral bond -71: Violation occurred on line 161 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp -71: Failed Expression: bnd -71: ---------- -71: Stacktrace: -71: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -71: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -71: 2# 0x0000FFFFA8DB7F04 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -71: 3# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -71: 4# 0x0000AAAAB4DE3120 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -71: 5# 0x0000AAAAB4DE1EF4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -71: 6# 0x0000FFFFA83C229C in /lib/aarch64-linux-gnu/libc.so.6 -71: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -71: 8# 0x0000AAAAB4DE21B0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -71: ---------- -71: **** -71: -71: [02:22:47] Finished: testGitHub2881() -71: [02:22:47] ----------------------------------------- -71: -71: [02:22:47] ----------------------------------------- -68: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -68: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -68: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -68: [02:22:47] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -71: [02:22:47] Finished: testGitHub3517() -71: [02:22:47] ----------------------------------------- -71: - 62/230 Test #71: testMolSupplier ........................ Passed 0.40 sec -test 74 - Start 74: testMolWriter - -74: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolWriter -74: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -74: Test timeout computed to be: 1500 -68: [02:22:47] deprecated group abbreviation ignored on line 24 -68: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] -68: [02:22:47] -68: -68: **** -68: Post-condition Violation -68: Element 'Mv' not found -68: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -68: Failed Expression: anum > -1 -68: ---------- -68: Stacktrace: -68: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -68: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -68: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -68: 3# 0x0000FFFF805A7CC4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -68: 4# 0x0000FFFF805B58A0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -68: 5# 0x0000FFFF805B67CC in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -68: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -68: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -68: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -68: 9# 0x0000AAAAC6F2F15C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: 10# 0x0000AAAAC6FA4464 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: 11# 0x0000AAAAC6F15578 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: 12# 0x0000FFFF7FC8229C in /lib/aarch64-linux-gnu/libc.so.6 -68: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -68: 14# 0x0000AAAAC6F157B0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: ---------- -68: **** -68: +67: [23:09:33] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 67: Test 67: 67: JDQ443_3d.mrv @@ -20488,7 +20142,7 @@ 67: 67: JDQ443_atropBad1.mrv 67: -67: [02:22:47] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +67: [23:09:33] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 67: Test 67: 67: RP-6306_atrop1.mrv @@ -20509,22 +20163,20 @@ 67: 67: RP-6306_atrop5.mrv 67: -67: [02:22:48] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -67: [02:22:48] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +67: [23:09:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +67: [23:09:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 67: Test 67: 67: RP-6306_atropBad1.mrv 67: -67: [02:22:48] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +67: [23:09:34] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 67: Test 67: 67: RP-6306_atropBad2.mrv 67: -67: [02:22:48] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -67: [02:22:48] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -67: [02:22:48] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -39: [02:22:48] done: 500000 -39: [02:22:48] Done +67: [23:09:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +67: [23:09:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +67: [23:09:34] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 67: Test 67: 67: RP-6306_3d.mrv @@ -20549,18 +20201,28 @@ 67: 67: Sotorasib_atrop5.mrv 67: -67: [02:22:48] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -67: [02:22:48] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +67: [23:09:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +67: [23:09:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 67: Test 67: 67: Sotorasib_atropBad1.mrv 67: -67: [02:22:48] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +67: [23:09:34] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 67: Test 67: 67: Sotorasib_atropBad2.mrv 67: -67: [02:22:48] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +67: [23:09:34] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +69: Atropisomers- 1 hits 3 misses +69: Final results: +69: Found atropisomers in TestMultInSDF.sdf - 1 hits 4 misses + 58/230 Test #69: testAtropisomers ....................... Passed 0.63 sec +test 70 + Start 70: testSquiggleDoubleBonds + +70: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testSquiggleDoubleBonds +70: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +70: Test timeout computed to be: 1500 67: Test 67: 67: Sotorasib_3d.mrv @@ -20581,20 +20243,18 @@ 67: 67: ZM374979_atropBad1.mrv 67: -67: [02:22:48] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -39: [02:22:48] Testing hanoi with a functor. -39: [02:22:48] Done -39: [02:22:48] Testing basic partition refinement. -39: [02:22:48] Done -39: [02:22:48] Testing partition refinement with neighbors. -39: [02:22:48] Done -39: [02:22:48] testing canonicalization via tie breaking. -39: [02:22:48] Done -39: [02:22:48] testing canonicalization using the wrapper. -68: [02:22:48] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -68: [02:22:48] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -39: [02:22:48] Done -39: [02:22:48] testing some specific ordering problems +67: [23:09:34] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +70: Randomness seeded to: 1551098781 +70: =============================================================================== +70: All tests passed (15 assertions in 3 test cases) +70: + 59/230 Test #70: testSquiggleDoubleBonds ................ Passed 0.10 sec +test 71 + Start 71: testMolSupplier + +71: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +71: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +71: Test timeout computed to be: 1500 67: Test 67: 67: mrtx1719_3d.mrv @@ -20615,45 +20275,33 @@ 67: 67: mrtx1719_atropBad1.mrv 67: -67: [02:22:48] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -39: [02:22:48] Finished -39: [02:22:48] testing chiral invariants. -39: [02:22:48] Finished -39: [02:22:48] testing unique ranks in w.r.t. renumbering. -39: [02:22:48] Finished -39: [02:22:48] testing mol fragments. -39: [02:22:48] Finished -39: [02:22:48] testing protein round-tripping. -59: Test -59: -59: AtropCanon1.cxsmi -59: -59: Test -59: -59: AtropCanon2.cxsmi -59: -59: Test -59: -59: AtropCanon3.cxsmi -59: -59: Test -59: -59: BMS-986142_3d_chiral.cxsmi -59: -59: Test -59: -59: BMS-986142_3d.cxsmi -59: -59: =============================================================================== -59: All tests passed (2445 assertions in 29 test cases) -59: - 63/230 Test #59: cxsmilesTest ........................... Passed 1.83 sec -test 75 - Start 75: testTplParser - -75: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testTplParser -75: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -75: Test timeout computed to be: 1500 +67: [23:09:34] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +66: ..............[23:09:34] SMILES Parse Error: syntax error while parsing: invalidsmiles +66: [23:09:34] SMILES Parse Error: Failed parsing SMILES 'invalidsmiles' for input: 'invalidsmiles' +71: [23:09:34] +71: ----------------------------------------- +71: [23:09:34] +71: +71: **** +71: Invariant Violation +71: bad prop value +71: Violation occurred on line 155 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp +71: Failed Expression: nSwaps < 2 +71: ---------- +71: Stacktrace: +71: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +71: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +71: 2# 0x0000FFFFA80879D8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +71: 3# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +71: 4# 0x0000AAAAC9A5E17C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +71: 5# 0x0000AAAAC9A52528 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +71: 6# 0x0000AAAAC9A20874 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +71: 7# 0x0000FFFFA769229C in /lib/aarch64-linux-gnu/libc.so.6 +71: 8# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +71: 9# 0x0000AAAAC9A221B0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +71: ---------- +71: **** +71: 67: Test 67: 67: FalseAtropisomer.mrv @@ -20710,17 +20358,8 @@ 67: 67: BMS-986142_atrop5.mrv 67: -67: [02:22:48] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -67: [02:22:48] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -27: -27: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... - 64/230 Test #75: testTplParser .......................... Passed 0.04 sec -test 76 - Start 76: testMol2ToMol - -76: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMol2ToMol -76: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -76: Test timeout computed to be: 1500 +67: [23:09:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +67: [23:09:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 67: Test 67: 67: BMS-986142_atrop6.mrv @@ -20733,65 +20372,635 @@ 67: 67: BMS-986142_atrop8.mrv 67: -67: [02:22:48] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -67: [02:22:48] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +67: [23:09:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +67: [23:09:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 67: Test 67: 67: BMS-986142_atropBad2.mrv 67: -67: [02:22:48] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -68: ---------------------------------- - 65/230 Test #76: testMol2ToMol .......................... Passed 0.04 sec -test 77 - Start 77: testSequence +67: [23:09:34] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +67: Test +67: +67: JDQ443_3d.mrv +67: +67: Test +67: +67: JDQ443_atrop1.mrv +67: +67: Test +67: +67: JDQ443_atrop2.mrv +67: +67: Test +67: +67: JDQ443_atrop3.mrv +67: +67: Test +67: +67: JDQ443_atropBad1.mrv +67: +67: [23:09:34] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +71: [23:09:34] Finished: testMolSup() +71: [23:09:34] ----------------------------------------- +71: +71: [23:09:34] ----------------------------------------- +71: [23:09:34] Finished: testRandMolSup() +71: [23:09:34] ----------------------------------------- +71: +71: [23:09:34] ----------------------------------------- +67: Test +67: +67: RP-6306_atrop1.mrv +67: +67: Test +67: +67: RP-6306_atrop2.mrv +67: +67: Test +67: +67: RP-6306_atrop3.mrv +67: +67: Test +67: +67: RP-6306_atrop4.mrv +67: +67: Test +67: +67: RP-6306_atrop5.mrv +67: +67: [23:09:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +67: [23:09:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +67: Test +67: +67: RP-6306_atropBad1.mrv +67: +67: [23:09:34] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +67: Test +67: +67: RP-6306_atropBad2.mrv +67: +67: [23:09:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +67: [23:09:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +67: [23:09:34] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +71: [23:09:34] Finished: testSmilesSup() +71: [23:09:34] ----------------------------------------- +71: +71: [23:09:34] ----------------------------------------- +71: [23:09:34] ------------------------------------------------------ +71: [23:09:34] SMILES Parse Error: syntax error while parsing: fail +71: [23:09:34] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +71: [23:09:34] ERROR: Smiles parse error on line 3 +71: [23:09:34] ERROR: Cannot create molecule from : 'fail' +71: [23:09:34] ------------------------------------------------------ +71: [23:09:34] ------------------------------------------------------ +71: [23:09:34] >>> This may result in an infinite loop. It should finish almost immediately: +71: [23:09:34] <<< done. +71: [23:09:34] Finished: testSmilesSupFromText() +71: [23:09:34] ----------------------------------------- +71: +71: [23:09:34] ----------------------------------------- +71: [23:09:34] Finished: testSmilesWriter() +71: [23:09:34] ----------------------------------------- +71: +71: [23:09:34] ----------------------------------------- +66: ..... +66: ---------------------------------------------------------------------- +66: Ran 19 tests in 1.150s +66: +66: OK +67: Test +67: +67: RP-6306_3d.mrv +67: +67: Test +67: +67: Sotorasib_atrop1.mrv +67: +67: Test +67: +67: Sotorasib_atrop2.mrv +67: +67: Test +67: +67: Sotorasib_atrop3.mrv +67: +67: Test +67: +67: Sotorasib_atrop4.mrv +67: +67: Test +67: +67: Sotorasib_atrop5.mrv +67: +67: [23:09:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +67: [23:09:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +67: Test +67: +67: Sotorasib_atropBad1.mrv +67: +67: [23:09:34] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +71: [23:09:34] Finished: testSDWriter() +71: [23:09:34] ----------------------------------------- +71: +71: [23:09:34] ----------------------------------------- +71: [23:09:34] Finished: testSDSupplierEnding() +71: [23:09:34] ----------------------------------------- +71: +71: [23:09:34] ----------------------------------------- +71: [23:09:34] Finished: testSuppliersEmptyFile() +71: [23:09:34] ----------------------------------------- +71: +71: [23:09:34] ----------------------------------------- +71: [23:09:34] Finished: testCisTrans() +71: [23:09:34] ----------------------------------------- +71: +71: [23:09:34] ----------------------------------------- +71: [23:09:34] Finished: testStereoRound() +71: [23:09:34] ----------------------------------------- +71: +71: [23:09:34] ----------------------------------------- +71: [23:09:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [23:09:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +67: Test +67: +67: Sotorasib_atropBad2.mrv +67: +67: [23:09:34] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +71: [23:09:34] Finished: testIssue226() +71: [23:09:34] ----------------------------------------- +71: +71: [23:09:34] ----------------------------------------- +71: [23:09:34] Finished: testTDTSupplier1() +71: [23:09:34] ----------------------------------------- +71: +71: [23:09:34] ----------------------------------------- +71: [23:09:34] Finished: testTDTSupplier2() +71: [23:09:34] ----------------------------------------- +71: +71: [23:09:34] ----------------------------------------- +71: [23:09:34] Finished: testTDTSupplier3() +71: [23:09:34] ----------------------------------------- +71: +71: [23:09:34] ----------------------------------------- +71: [23:09:34] Finished: testSDSupplierFromText() +71: [23:09:34] ----------------------------------------- +71: +71: [23:09:34] ----------------------------------------- +71: [23:09:34] ERROR: Problems encountered parsing data fields +71: [23:09:34] ERROR: moving to the beginning of the next molecule +71: [23:09:34] ERROR: Problems encountered parsing data fields +71: [23:09:34] ERROR: moving to the beginning of the next molecule +71: [23:09:34] Spurious data before the first property will be ignored +71: [23:09:34] Property will be truncated after the first blank line +71: [23:09:34] Property will be truncated after the first blank line +71: [23:09:34] Property will be truncated after the first blank line +71: [23:09:34] Finished: testSDSupplierStrLax1() +71: [23:09:34] ----------------------------------------- +71: +71: [23:09:34] ----------------------------------------- +71: [23:09:34] ERROR: Problems encountered parsing data fields +71: [23:09:34] ERROR: moving to the beginning of the next molecule +71: [23:09:34] Property will be truncated after the first blank line +71: [23:09:34] Finished: testSDSupplierStrLax2() +71: [23:09:34] ----------------------------------------- +71: +71: [23:09:34] ----------------------------------------- +71: [23:09:34] ERROR: Problems encountered parsing data fields +71: [23:09:34] ERROR: moving to the beginning of the next molecule +71: [23:09:34] ERROR: Problems encountered parsing data fields +71: [23:09:34] ERROR: moving to the beginning of the next molecule +71: [23:09:34] Spurious data before the first property will be ignored +71: [23:09:34] Property will be truncated after the first blank line +71: [23:09:34] Property will be truncated after the first blank line +71: [23:09:34] Property will be truncated after the first blank line +71: [23:09:34] Finished: testSDSupplierFromTextStrLax1() +71: [23:09:34] ----------------------------------------- +71: +71: [23:09:34] ----------------------------------------- +71: [23:09:34] ERROR: Problems encountered parsing data fields +71: [23:09:34] ERROR: moving to the beginning of the next molecule +71: [23:09:34] Property will be truncated after the first blank line +71: [23:09:34] Finished: testSDSupplierFromTextStrLax2() +71: [23:09:34] ----------------------------------------- +71: +71: [23:09:34] ----------------------------------------- +71: [23:09:34] Finished: testIssue265() +71: [23:09:34] ----------------------------------------- +71: +71: [23:09:34] ----------------------------------------- +71: [23:09:34] ERROR: End of data field name not found +71: [23:09:34] ERROR: moving to the beginning of the next molecule +71: [23:09:34] Explicit valence for atom # 0 F, 2, is greater than permitted +71: [23:09:34] ERROR: Could not sanitize molecule ending on line 16 +71: [23:09:34] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted +71: [23:09:34] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 +71: [23:09:34] ERROR: moving to the beginning of the next molecule +71: [23:09:34] ERROR: Bond line too short: 'M END' on line 18 +71: [23:09:34] ERROR: moving to the beginning of the next molecule +71: [23:09:34] Finished: testSDErrorHandling() +71: [23:09:34] ----------------------------------------- +71: +71: [23:09:34] ----------------------------------------- +71: [23:09:34] Finished: testIssue381() +71: [23:09:34] ----------------------------------------- +71: +71: [23:09:34] ----------------------------------------- +71: [23:09:34] Finished: testSetStreamIndices() +71: [23:09:34] ----------------------------------------- +71: +71: [23:09:34] ----------------------------------------- +71: [23:09:34] Finished: testMixIterAndRandom() +71: [23:09:34] ----------------------------------------- +71: +71: [23:09:34] ----------------------------------------- +71: build: +71: [23:09:34] Finished: testRemoveHs() +71: [23:09:34] ----------------------------------------- +71: +71: [23:09:34] ----------------------------------------- +71: [23:09:34] Finished: testGetItemText() +71: [23:09:34] ----------------------------------------- +71: +71: [23:09:34] ----------------------------------------- +71: [23:09:34] Finished: testForwardSDSupplier() +71: [23:09:34] ----------------------------------------- +71: +71: [23:09:34] ----------------------------------------- +71: [23:09:34] Finished: testMissingCRSDSupplier() +71: [23:09:34] ----------------------------------------- +71: +71: [23:09:34] ----------------------------------------- +71: [23:09:34] Finished: testIssue3482695() +71: [23:09:34] ----------------------------------------- +71: +71: [23:09:34] ----------------------------------------- +71: [23:09:34] ERROR: Cannot convert 'foo' to unsigned int on line 557 +71: [23:09:34] ERROR: moving to the beginning of the next molecule +71: [23:09:34] Finished: testIssue3525673() +71: [23:09:34] ----------------------------------------- +71: +71: [23:09:34] ----------------------------------------- +71: [23:09:34] Finished: testBlankLinesInProps() +71: [23:09:34] ----------------------------------------- +71: +71: [23:09:34] ----------------------------------------- +71: [23:09:34] Finished: testSkipLines() +71: [23:09:34] ----------------------------------------- +71: +71: [23:09:34] ----------------------------------------- +71: [23:09:34] Finished: testGitHub23() +71: [23:09:34] ----------------------------------------- +71: +71: [23:09:34] ----------------------------------------- +71: [23:09:34] Finished: testGitHub88() +71: [23:09:34] ----------------------------------------- +71: +71: [23:09:34] ----------------------------------------- +67: Test +67: +67: Sotorasib_3d.mrv +67: +67: Test +67: +67: ZM374979_atrop1.mrv +67: +67: Test +67: +67: ZM374979_atrop2.mrv +67: +67: Test +67: +67: ZM374979_atrop3.mrv +67: +67: Test +67: +67: ZM374979_atropBad1.mrv +67: +67: [23:09:34] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +59: Test +59: +59: AtropCanon1.cxsmi +59: +59: Test +59: +59: AtropCanon2.cxsmi +59: +59: Test +59: +59: AtropCanon3.cxsmi +59: +59: Test +59: +59: BMS-986142_3d_chiral.cxsmi +59: +59: Test +59: +59: BMS-986142_3d.cxsmi +59: +59: =============================================================================== +59: All tests passed (2445 assertions in 29 test cases) +59: + 60/230 Test #59: cxsmilesTest ........................... Passed 2.82 sec +test 72 + Start 72: testGeneralFileReader -77: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testSequence -77: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -77: Test timeout computed to be: 1500 -68: ---------------------------------- -68: [02:22:48] +72: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader +72: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +72: Test timeout computed to be: 1500 +71: [23:09:34] Finished: testGitHub2285() +71: [23:09:34] ----------------------------------------- +71: +71: [23:09:34] ----------------------------------------- +71: [23:09:34] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +71: [23:09:34] ERROR: Smiles parse error on line 1 +71: [23:09:34] ERROR: Cannot create molecule from : 'c1ccccc' +71: [23:09:34] SMILES Parse Error: extra open parentheses for input: 'C(C' +71: [23:09:34] ERROR: Smiles parse error on line 3 +71: [23:09:34] ERROR: Cannot create molecule from : 'C(C' +71: [23:09:34] Explicit valence for atom # 1 C, 5, is greater than permitted +71: [23:09:34] ERROR: Could not sanitize molecule on line 5 +71: [23:09:34] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +71: [23:09:34] Explicit valence for atom # 1 F, 2, is greater than permitted +71: [23:09:34] ERROR: Could not sanitize molecule ending on line 21 +71: [23:09:34] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +71: [23:09:34] Explicit valence for atom # 1 F, 2, is greater than permitted +71: [23:09:34] ERROR: Could not sanitize molecule ending on line 21 +71: [23:09:34] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +71: [23:09:34] Explicit valence for atom # 1 F, 2, is greater than permitted +71: [23:09:34] ERROR: Could not sanitize molecule ending on line 21 +71: [23:09:34] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +71: [23:09:34] ERROR: Atom line too short: ' -9.6' on line 28 +71: [23:09:34] ERROR: moving to the beginning of the next molecule +71: [23:09:34] Explicit valence for atom # 1 F, 2, is greater than permitted +71: [23:09:34] ERROR: Could not sanitize molecule ending on line 21 +71: [23:09:34] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +71: [23:09:34] ERROR: Atom line too short: ' -9.6' on line 28 +71: [23:09:34] ERROR: moving to the beginning of the next molecule +71: [23:09:34] Finished: testGitHub2479() +71: [23:09:34] ----------------------------------------- +71: +71: [23:09:34] ----------------------------------------- +71: [23:09:34] +71: +71: **** +71: Invariant Violation +71: bad chiral bond +71: Violation occurred on line 161 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp +71: Failed Expression: bnd +71: ---------- +71: Stacktrace: +71: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +71: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +71: 2# 0x0000FFFFA8087F04 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +71: 3# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +71: 4# 0x0000AAAAC9A23120 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +71: 5# 0x0000AAAAC9A21EF4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +71: 6# 0x0000FFFFA769229C in /lib/aarch64-linux-gnu/libc.so.6 +71: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +71: 8# 0x0000AAAAC9A221B0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +71: ---------- +71: **** +71: +71: [23:09:34] Finished: testGitHub2881() +71: [23:09:34] ----------------------------------------- +71: +71: [23:09:34] ----------------------------------------- +71: [23:09:34] Finished: testGitHub3517() +71: [23:09:34] ----------------------------------------- +71: + 61/230 Test #71: testMolSupplier ........................ Passed 0.58 sec +test 73 + Start 73: testMultithreadedMolSupplier + +73: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier +73: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +73: Test timeout computed to be: 1500 +67: Test +67: +67: mrtx1719_3d.mrv +67: +67: Test +67: +67: mrtx1719_atrop1.mrv +67: +67: Test +67: +67: mrtx1719_atrop2.mrv +67: +67: Test +67: +67: mrtx1719_atrop3.mrv +67: +67: Test +67: +67: mrtx1719_atropBad1.mrv +67: +67: [23:09:34] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +72: [23:09:34] +72: ----------------------------------------- +72: [23:09:34] Finished: testDetermineFormat() +72: [23:09:34] ----------------------------------------- +72: +72: [23:09:34] +72: ----------------------------------------- +73: [23:09:34] +73: ----------------------------------------- + 62/230 Test #66: pyDepictor ............................. Passed 2.43 sec +test 74 + Start 74: testMolWriter + +74: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolWriter +74: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +74: Test timeout computed to be: 1500 +72: [23:09:34] Finished: testSdf() +72: [23:09:34] ----------------------------------------- +72: +72: [23:09:34] +72: ----------------------------------------- +67: Test +67: +67: AlexRxn.mrv +67: +67: Test +67: +67: BadReactionSign.mrv +67: +67: Test +67: +67: bondArray_node.mrv +67: +67: Test +67: +67: marvin03.mrv +67: +67: Test +67: +67: marvin04.mrv +67: +67: Test +67: +67: marvin08.mrv +67: +67: Test +67: +67: marvin09.mrv +67: +67: Test +67: +67: marvin11.mrv +67: +67: Test +67: +67: marvin05.mrv +67: +67: Test +67: +67: EmptyRxn.mrv +67: +67: [23:09:34] initialization failed +68: [23:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +68: [23:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +68: [23:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +68: [23:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +68: [23:09:35] deprecated group abbreviation ignored on line 24 +68: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] +68: [23:09:35] 68: 68: **** -68: Pre-condition Violation -68: rlabel out of range for MDL files -68: Violation occurred on line 857 in file ./Code/GraphMol/Atom.cpp -68: Failed Expression: rlabel >= 0 && rlabel < 100 +68: Post-condition Violation +68: Element 'Mv' not found +68: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h +68: Failed Expression: anum > -1 68: ---------- 68: Stacktrace: 68: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 68: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -68: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -68: 3# 0x0000AAAAC6F3EC20 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: 4# 0x0000AAAAC6FA44C4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: 5# 0x0000AAAAC6F15578 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: 6# 0x0000FFFF7FC8229C in /lib/aarch64-linux-gnu/libc.so.6 -68: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -68: 8# 0x0000AAAAC6F157B0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +68: 3# 0x0000FFFF959B7CC4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +68: 4# 0x0000FFFF959C58A0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +68: 5# 0x0000FFFF959C67CC in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +68: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +68: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +68: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +68: 9# 0x0000AAAACADFF15C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 10# 0x0000AAAACAE74464 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 11# 0x0000AAAACADE5578 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 12# 0x0000FFFF9509229C in /lib/aarch64-linux-gnu/libc.so.6 +68: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +68: 14# 0x0000AAAACADE57B0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 68: ---------- 68: **** 68: -68: [02:22:48] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 67: Test 67: -67: JDQ443_3d.mrv +67: RxnNoCoords.mrv 67: 67: Test 67: -67: JDQ443_atrop1.mrv +67: mrvValenceZero.mrv 67: 67: Test 67: -67: JDQ443_atrop2.mrv +67: condition_coordinates_mpoint.mrv 67: 67: Test 67: -67: JDQ443_atrop3.mrv +67: marvin01.mrv 67: 67: Test 67: -67: JDQ443_atropBad1.mrv +67: aspirineSynthesisWithAttributes.mrv +67: +67: Test 67: -67: [02:22:48] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +67: marvin01.mrv +67: +67: Test +67: +67: NewChiralTest +67: +67: Test +67: +67: NewChiralTest +67: +67: Test +67: +67: NewChiralTestNoChiral +67: +67: Test +67: +67: NewChiralTestNoChiral +67: +67: Test +67: +67: NewChiralTest2 +67: +67: Test +67: +67: NewChiralTest2 +67: +67: Test +67: +67: NewChiralTest2AllChiral +67: +67: Test +67: +67: NewChiralTest2AllChiral +67: +67: Test +67: +67: Vendor839 +67: +67: Test +67: +67: DoubleBondChain +67: +67: Test +67: +67: Na_Mg_Al_OH +67: +67: Test +67: +67: Pb +67: +67: Test +67: +67: O_Mg_Si +67: +67: Test +67: +67: SquiggleBond +67: +67: Test +67: +67: BigMacrocycle +67: +67: Test +67: +67: Smiles1 +67: + 63/230 Test #67: testMrvToMol ........................... Passed 2.32 sec +test 75 + Start 75: testTplParser + +75: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testTplParser +75: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +75: Test timeout computed to be: 1500 + 64/230 Test #75: testTplParser .......................... Passed 0.10 sec +test 76 + Start 76: testMol2ToMol + +76: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMol2ToMol +76: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +76: Test timeout computed to be: 1500 + 65/230 Test #76: testMol2ToMol .......................... Passed 0.11 sec +test 77 + Start 77: testSequence + +77: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testSequence +77: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +77: Test timeout computed to be: 1500 +27: Checking against /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 77: Sequence: GREG 77: HELM: PEPTIDE1{G.R.E.G}$$$$ 77: Smiles: N=C(N)NCCC[C@H](NC(=O)CN)C(=O)N[C@@H](CCC(=O)O)C(=O)NCC(=O)O @@ -21422,6 +21631,8 @@ 77: ATOM 19 O GLU A 3 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 20 CB GLU A 3 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 21 CG GLU A 3 0.000 0.000 0.000 1.00 0.00 C +68: [23:09:35] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +68: [23:09:35] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 77: ATOM 22 CD GLU A 3 0.000 0.000 0.000 1.00 0.00 C 77: ATOM 23 OE1 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 77: ATOM 24 OE2 GLU A 3 0.000 0.000 0.000 1.00 0.00 O @@ -21776,48 +21987,7 @@ 77: CONECT 27 28 28 29 77: END 77: - 66/230 Test #77: testSequence ........................... Passed 0.04 sec -test 78 - Start 78: testExtendedStereoParsing - -78: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testExtendedStereoParsing -78: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -78: Test timeout computed to be: 1500 -67: Test -67: -67: RP-6306_atrop1.mrv -67: -67: Test -67: -67: RP-6306_atrop2.mrv -67: -67: Test -67: -67: RP-6306_atrop3.mrv -67: -67: Test -67: -67: RP-6306_atrop4.mrv -67: -67: Test -67: -67: RP-6306_atrop5.mrv -67: -67: [02:22:48] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -67: [02:22:48] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -67: Test -67: -67: RP-6306_atropBad1.mrv -67: -67: [02:22:48] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -67: Test -67: -67: RP-6306_atropBad2.mrv -67: -67: [02:22:48] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -67: [02:22:48] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -67: [02:22:48] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -74: [02:22:48] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +74: [23:09:35] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 74: 0.40201265 0.40201265 74: -0.13299436 -0.13299436 74: 1.00000017 1.00000017 @@ -21839,78 +22009,49 @@ 74: 3.0077234 3.0077234 74: 0.37399312 0.37399312 74: -0.07713336 -0.07713336 -74: [02:22:48] bond with order 0 found on line 11. This is not part of the MDL specification. -74: [02:22:48] bond with order 0 found on line 16. This is not part of the MDL specification. - 67/230 Test #78: testExtendedStereoParsing .............. Passed 0.05 sec + 66/230 Test #77: testSequence ........................... Passed 0.13 sec +test 78 + Start 78: testExtendedStereoParsing + +78: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testExtendedStereoParsing +78: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +78: Test timeout computed to be: 1500 +74: [23:09:35] bond with order 0 found on line 11. This is not part of the MDL specification. +74: [23:09:35] bond with order 0 found on line 16. This is not part of the MDL specification. + 67/230 Test #74: testMolWriter .......................... Passed 0.54 sec test 79 Start 79: fileParsersCatchTest 79: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 79: Test timeout computed to be: 1500 -67: Test -67: -67: RP-6306_3d.mrv -67: -67: Test -67: -67: Sotorasib_atrop1.mrv -67: -67: Test -67: -67: Sotorasib_atrop2.mrv -67: -67: Test -67: -67: Sotorasib_atrop3.mrv -67: -67: Test -67: -67: Sotorasib_atrop4.mrv -67: -67: Test -67: -67: Sotorasib_atrop5.mrv -67: -67: [02:22:48] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -67: [02:22:48] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -67: Test -67: -67: Sotorasib_atropBad1.mrv -67: -67: [02:22:48] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 - 68/230 Test #74: testMolWriter .......................... Passed 0.45 sec + 68/230 Test #78: testExtendedStereoParsing .............. Passed 0.08 sec test 80 Start 80: testPropertyLists 80: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testPropertyLists 80: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 80: Test timeout computed to be: 1500 -67: Test -67: -67: Sotorasib_atropBad2.mrv -67: -67: [02:22:48] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -79: Randomness seeded to: 3999208636 -79: [02:22:48] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 -79: [02:22:48] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -79: [02:22:48] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -79: [02:22:48] SGroup 1 is invalid and will be ignored -79: [02:22:48] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -79: [02:22:48] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -79: [02:22:48] SGroup 1 is invalid and will be ignored -79: [02:22:48] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 -79: [02:22:48] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -79: [02:22:48] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -79: [02:22:48] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 -79: [02:22:48] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -79: [02:22:48] SGroup 1 is invalid and will be ignored -79: [02:22:48] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -79: [02:22:48] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -79: [02:22:48] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -79: [02:22:48] SGroup 1 is invalid and will be ignored -79: [02:22:48] SGroup 3 referenced on line 40 not found. -79: [02:22:48] +79: Randomness seeded to: 2736844703 +79: [23:09:35] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 +79: [23:09:35] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +79: [23:09:35] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +79: [23:09:35] SGroup 1 is invalid and will be ignored +79: [23:09:35] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +79: [23:09:35] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +79: [23:09:35] SGroup 1 is invalid and will be ignored +79: [23:09:35] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 +79: [23:09:35] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +79: [23:09:35] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +79: [23:09:35] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 +79: [23:09:35] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +79: [23:09:35] SGroup 1 is invalid and will be ignored +79: [23:09:35] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +79: [23:09:35] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +79: [23:09:35] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +79: [23:09:35] SGroup 1 is invalid and will be ignored +79: [23:09:35] SGroup 3 referenced on line 40 not found. +79: [23:09:35] 79: 79: **** 79: Pre-condition Violation @@ -21923,24 +22064,24 @@ 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 3# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 4# 0x0000FFFF952CEB68 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 4# 0x0000FFFFA12CEB68 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 5# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 7# 0x0000AAAAD0927B7C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 8# 0x0000AAAAD099C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x0000AAAAD099D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000AAAAD099D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000AAAAD0970A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000AAAAD0970F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000AAAAD08EB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x0000FFFF949A229C in /lib/aarch64-linux-gnu/libc.so.6 +79: 7# 0x0000AAAABB407B7C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 8# 0x0000AAAABB47C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x0000AAAABB47D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x0000AAAABB47D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x0000AAAABB450A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x0000AAAABB450F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x0000AAAABB3CB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x0000FFFFA09A229C in /lib/aarch64-linux-gnu/libc.so.6 79: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -79: 16# 0x0000AAAAD08EB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0x0000AAAABB3CB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [02:22:48] SGroup 3 referenced on line 40 not found. -79: [02:22:48] +79: [23:09:35] SGroup 3 referenced on line 40 not found. +79: [23:09:35] 79: 79: **** 79: Pre-condition Violation @@ -21953,29 +22094,29 @@ 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 3# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 4# 0x0000FFFF952CEB68 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 4# 0x0000FFFFA12CEB68 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 5# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 7# 0x0000AAAAD0927BFC in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 8# 0x0000AAAAD099C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x0000AAAAD099D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000AAAAD099D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000AAAAD0970A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000AAAAD0970F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000AAAAD08EB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x0000FFFF949A229C in /lib/aarch64-linux-gnu/libc.so.6 +79: 7# 0x0000AAAABB407BFC in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 8# 0x0000AAAABB47C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x0000AAAABB47D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x0000AAAABB47D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x0000AAAABB450A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x0000AAAABB450F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x0000AAAABB3CB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x0000FFFFA09A229C in /lib/aarch64-linux-gnu/libc.so.6 79: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -79: 16# 0x0000AAAAD08EB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0x0000AAAABB3CB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [02:22:48] no bonds -79: [02:22:48] SGroup 1 is invalid and will be ignored -79: [02:22:48] SGroup line too short: 'M SBV 1 6' on line 42 -79: [02:22:48] SGroup 1 is invalid and will be ignored -79: [02:22:48] SGroup line too short: 'M SBL 2 3 9 10' on line 46 -79: [02:22:48] SGroup 2 is invalid and will be ignored -79: [02:22:48] +79: [23:09:35] no bonds +79: [23:09:35] SGroup 1 is invalid and will be ignored +79: [23:09:35] SGroup line too short: 'M SBV 1 6' on line 42 +79: [23:09:35] SGroup 1 is invalid and will be ignored +79: [23:09:35] SGroup line too short: 'M SBL 2 3 9 10' on line 46 +79: [23:09:35] SGroup 2 is invalid and will be ignored +79: [23:09:35] 79: 79: **** 79: Pre-condition Violation @@ -21989,36 +22130,25 @@ 79: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 5# 0x0000FFFF952CEAD0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 5# 0x0000FFFFA12CEAD0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 8# 0x0000AAAAD09285A4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x0000AAAAD099C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000AAAAD099D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000AAAAD099D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000AAAAD0970A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000AAAAD0970F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x0000AAAAD08EB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x0000FFFF949A229C in /lib/aarch64-linux-gnu/libc.so.6 +79: 8# 0x0000AAAABB4085A4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x0000AAAABB47C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x0000AAAABB47D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x0000AAAABB47D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x0000AAAABB450A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x0000AAAABB450F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x0000AAAABB3CB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x0000FFFFA09A229C in /lib/aarch64-linux-gnu/libc.so.6 79: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -79: 17# 0x0000AAAAD08EB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 17# 0x0000AAAABB3CB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [02:22:48] +79: [23:09:35] 79: 79: **** -80: Randomness seeded to: 2630811393 -80: =============================================================================== -80: All tests passed (95 assertions in 4 test cases) -80: - 69/230 Test #80: testPropertyLists ...................... Passed 0.04 sec -test 81 - Start 81: XYZFileParserCatchTest - -81: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/XYZFileParserCatchTest -81: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -81: Test timeout computed to be: 1500 79: Pre-condition Violation 79: bookmark not found 79: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp @@ -22030,24 +22160,24 @@ 79: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 5# 0x0000FFFF952CEAD0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 5# 0x0000FFFFA12CEAD0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 8# 0x0000AAAAD0928624 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x0000AAAAD099C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000AAAAD099D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000AAAAD099D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000AAAAD0970A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000AAAAD0970F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x0000AAAAD08EB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x0000FFFF949A229C in /lib/aarch64-linux-gnu/libc.so.6 +79: 8# 0x0000AAAABB408624 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x0000AAAABB47C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x0000AAAABB47D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x0000AAAABB47D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x0000AAAABB450A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x0000AAAABB450F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x0000AAAABB3CB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x0000FFFFA09A229C in /lib/aarch64-linux-gnu/libc.so.6 79: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -79: 17# 0x0000AAAAD08EB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 17# 0x0000AAAABB3CB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [02:22:48] bookmark not found -79: [02:22:48] +79: [23:09:35] bookmark not found +79: [23:09:35] 79: 79: **** 79: Pre-condition Violation @@ -22061,25 +22191,25 @@ 79: 2# RDKit::SubstanceGroup::getBondType(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 3# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 4# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 5# 0x0000FFFF952CEB68 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 5# 0x0000FFFFA12CEB68 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 8# 0x0000AAAAD0928624 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x0000AAAAD099C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000AAAAD099D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000AAAAD099D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000AAAAD0970A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000AAAAD0970F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x0000AAAAD08EB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x0000FFFF949A229C in /lib/aarch64-linux-gnu/libc.so.6 +79: 8# 0x0000AAAABB408624 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x0000AAAABB47C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x0000AAAABB47D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x0000AAAABB47D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x0000AAAABB450A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x0000AAAABB450F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x0000AAAABB3CB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x0000FFFFA09A229C in /lib/aarch64-linux-gnu/libc.so.6 79: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -79: 17# 0x0000AAAAD08EB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 17# 0x0000AAAABB3CB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [02:22:48] bond is not part of the SubstanceGroup -79: [02:22:48] SGroup 2 is invalid and will be ignored -79: [02:22:48] +79: [23:09:35] bond is not part of the SubstanceGroup +79: [23:09:35] SGroup 2 is invalid and will be ignored +79: [23:09:35] 79: 79: **** 79: Pre-condition Violation @@ -22093,23 +22223,23 @@ 79: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 5# 0x0000FFFF952CEAD0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 5# 0x0000FFFFA12CEAD0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 8# 0x0000AAAAD0928914 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x0000AAAAD099C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000AAAAD099D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000AAAAD099D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000AAAAD0970A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000AAAAD0970F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x0000AAAAD08EB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x0000FFFF949A229C in /lib/aarch64-linux-gnu/libc.so.6 +79: 8# 0x0000AAAABB408914 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x0000AAAABB47C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x0000AAAABB47D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x0000AAAABB47D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x0000AAAABB450A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x0000AAAABB450F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x0000AAAABB3CB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x0000FFFFA09A229C in /lib/aarch64-linux-gnu/libc.so.6 79: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -79: 17# 0x0000AAAAD08EB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 17# 0x0000AAAABB3CB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [02:22:48] +79: [23:09:35] 79: 79: **** 79: Pre-condition Violation @@ -22123,27 +22253,27 @@ 79: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 79: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 5# 0x0000FFFF952CEAD0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 5# 0x0000FFFFA12CEAD0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 8# 0x0000AAAAD0928994 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x0000AAAAD099C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000AAAAD099D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000AAAAD099D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000AAAAD0970A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000AAAAD0970F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x0000AAAAD08EB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x0000FFFF949A229C in /lib/aarch64-linux-gnu/libc.so.6 +79: 8# 0x0000AAAABB408994 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x0000AAAABB47C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x0000AAAABB47D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x0000AAAABB47D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x0000AAAABB450A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x0000AAAABB450F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x0000AAAABB3CB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x0000FFFFA09A229C in /lib/aarch64-linux-gnu/libc.so.6 79: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -79: 17# 0x0000AAAAD08EB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 17# 0x0000AAAABB3CB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [02:22:48] bookmark not found -79: [02:22:48] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. -79: [02:22:48] SGroup 2 is invalid and will be ignored -79: [02:22:48] WARNING: final character of V3000 array is not ')' -79: [02:22:48] +79: [23:09:35] bookmark not found +79: [23:09:35] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. +79: [23:09:35] SGroup 2 is invalid and will be ignored +79: [23:09:35] WARNING: final character of V3000 array is not ')' +79: [23:09:35] 79: 79: **** 79: Pre-condition Violation @@ -22161,21 +22291,21 @@ 79: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 9# 0x0000AAAAD0926598 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000AAAAD099C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000AAAAD099D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000AAAAD099D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000AAAAD0970A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x0000AAAAD0970F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x0000AAAAD08EB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 16# 0x0000FFFF949A229C in /lib/aarch64-linux-gnu/libc.so.6 +79: 9# 0x0000AAAABB406598 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x0000AAAABB47C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x0000AAAABB47D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x0000AAAABB47D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x0000AAAABB450A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x0000AAAABB450F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x0000AAAABB3CB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0x0000FFFFA09A229C in /lib/aarch64-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -79: 18# 0x0000AAAAD08EB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 18# 0x0000AAAABB3CB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [02:22:48] WARNING: final character of V3000 array is not ')' -79: [02:22:48] +79: [23:09:35] WARNING: final character of V3000 array is not ')' +79: [23:09:35] 79: 79: **** 79: Pre-condition Violation @@ -22193,23 +22323,23 @@ 79: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 9# 0x0000AAAAD0926614 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000AAAAD099C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000AAAAD099D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000AAAAD099D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000AAAAD0970A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x0000AAAAD0970F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x0000AAAAD08EB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 16# 0x0000FFFF949A229C in /lib/aarch64-linux-gnu/libc.so.6 +79: 9# 0x0000AAAABB406614 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x0000AAAABB47C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x0000AAAABB47D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x0000AAAABB47D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x0000AAAABB450A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x0000AAAABB450F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x0000AAAABB3CB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0x0000FFFFA09A229C in /lib/aarch64-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -79: 18# 0x0000AAAAD08EB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 18# 0x0000AAAABB3CB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [02:22:48] bookmark not found -79: [02:22:48] SGroup 1 is invalid and will be ignored -79: [02:22:48] WARNING: final character of V3000 array is not ')' -79: [02:22:48] +79: [23:09:35] bookmark not found +79: [23:09:35] SGroup 1 is invalid and will be ignored +79: [23:09:35] WARNING: final character of V3000 array is not ')' +79: [23:09:35] 79: 79: **** 79: Pre-condition Violation @@ -22227,21 +22357,21 @@ 79: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 9# 0x0000AAAAD09268E8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000AAAAD099C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000AAAAD099D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000AAAAD099D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000AAAAD0970A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x0000AAAAD0970F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x0000AAAAD08EB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 16# 0x0000FFFF949A229C in /lib/aarch64-linux-gnu/libc.so.6 +79: 9# 0x0000AAAABB4068E8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x0000AAAABB47C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x0000AAAABB47D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x0000AAAABB47D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x0000AAAABB450A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x0000AAAABB450F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x0000AAAABB3CB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0x0000FFFFA09A229C in /lib/aarch64-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -79: 18# 0x0000AAAAD08EB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 18# 0x0000AAAABB3CB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [02:22:48] WARNING: final character of V3000 array is not ')' -79: [02:22:48] +79: [23:09:35] WARNING: final character of V3000 array is not ')' +79: [23:09:35] 79: 79: **** 79: Pre-condition Violation @@ -22259,22 +22389,22 @@ 79: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 9# 0x0000AAAAD0926964 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000AAAAD099C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000AAAAD099D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000AAAAD099D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000AAAAD0970A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x0000AAAAD0970F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x0000AAAAD08EB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 16# 0x0000FFFF949A229C in /lib/aarch64-linux-gnu/libc.so.6 +79: 9# 0x0000AAAABB406964 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x0000AAAABB47C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x0000AAAABB47D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x0000AAAABB47D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x0000AAAABB450A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x0000AAAABB450F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x0000AAAABB3CB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0x0000FFFFA09A229C in /lib/aarch64-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -79: 18# 0x0000AAAAD08EB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 18# 0x0000AAAABB3CB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [02:22:48] bookmark not found -79: [02:22:48] SGroup 1 is invalid and will be ignored -79: [02:22:48] +79: [23:09:35] bookmark not found +79: [23:09:35] SGroup 1 is invalid and will be ignored +79: [23:09:35] 79: 79: **** 79: Pre-condition Violation @@ -22292,20 +22422,20 @@ 79: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 9# 0x0000AAAAD0926C38 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000AAAAD099C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000AAAAD099D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000AAAAD099D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000AAAAD0970A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x0000AAAAD0970F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x0000AAAAD08EB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 16# 0x0000FFFF949A229C in /lib/aarch64-linux-gnu/libc.so.6 +79: 9# 0x0000AAAABB406C38 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x0000AAAABB47C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x0000AAAABB47D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x0000AAAABB47D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x0000AAAABB450A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x0000AAAABB450F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x0000AAAABB3CB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0x0000FFFFA09A229C in /lib/aarch64-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -79: 18# 0x0000AAAAD08EB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 18# 0x0000AAAABB3CB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [02:22:48] +79: [23:09:35] 79: 79: **** 79: Pre-condition Violation @@ -22323,22 +22453,22 @@ 79: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 9# 0x0000AAAAD0926CB4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000AAAAD099C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000AAAAD099D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000AAAAD099D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000AAAAD0970A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x0000AAAAD0970F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x0000AAAAD08EB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 16# 0x0000FFFF949A229C in /lib/aarch64-linux-gnu/libc.so.6 +79: 9# 0x0000AAAABB406CB4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x0000AAAABB47C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x0000AAAABB47D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x0000AAAABB47D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x0000AAAABB450A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x0000AAAABB450F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x0000AAAABB3CB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0x0000FFFFA09A229C in /lib/aarch64-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -79: 18# 0x0000AAAAD08EB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 18# 0x0000AAAABB3CB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [02:22:48] bookmark not found -79: [02:22:48] SGroup 2 is invalid and will be ignored -79: [02:22:48] +79: [23:09:35] bookmark not found +79: [23:09:35] SGroup 2 is invalid and will be ignored +79: [23:09:35] 79: 79: **** 79: Pre-condition Violation @@ -22356,20 +22486,20 @@ 79: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 9# 0x0000AAAAD0926F88 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000AAAAD099C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000AAAAD099D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000AAAAD099D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000AAAAD0970A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x0000AAAAD0970F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x0000AAAAD08EB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 16# 0x0000FFFF949A229C in /lib/aarch64-linux-gnu/libc.so.6 +79: 9# 0x0000AAAABB406F88 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x0000AAAABB47C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x0000AAAABB47D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x0000AAAABB47D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x0000AAAABB450A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x0000AAAABB450F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x0000AAAABB3CB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0x0000FFFFA09A229C in /lib/aarch64-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -79: 18# 0x0000AAAAD08EB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 18# 0x0000AAAABB3CB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [02:22:48] +79: [23:09:35] 79: 79: **** 79: Pre-condition Violation @@ -22387,83 +22517,30 @@ 79: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 9# 0x0000AAAAD0927004 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000AAAAD099C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000AAAAD099D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000AAAAD099D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000AAAAD0970A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x0000AAAAD0970F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x0000AAAAD08EB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 16# 0x0000FFFF949A229C in /lib/aarch64-linux-gnu/libc.so.6 +79: 9# 0x0000AAAABB407004 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x0000AAAABB47C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x0000AAAABB47D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x0000AAAABB47D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x0000AAAABB450A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x0000AAAABB450F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x0000AAAABB3CB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0x0000FFFFA09A229C in /lib/aarch64-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -79: 18# 0x0000AAAAD08EB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 18# 0x0000AAAABB3CB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [02:22:48] bookmark not found -79: [02:22:48] SGroup 2 is invalid and will be ignored -67: Test -67: -67: Sotorasib_3d.mrv -67: -67: Test -67: -67: ZM374979_atrop1.mrv -67: -67: Test -67: -67: ZM374979_atrop2.mrv -67: -67: Test -67: -67: ZM374979_atrop3.mrv -67: -67: Test -67: -67: ZM374979_atropBad1.mrv -67: -67: [02:22:48] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -79: [02:22:48] Explicit valence for atom # 2 O, 3, is greater than permitted -79: [02:22:48] Explicit valence for atom # 1 O, 3, is greater than permitted -79: [02:22:48] Explicit valence for atom # 1 C, 5, is greater than permitted -81: Randomness seeded to: 1123417659 -81: =============================================================================== -81: All tests passed (100 assertions in 2 test cases) -81: - 70/230 Test #81: XYZFileParserCatchTest ................. Passed 0.03 sec -test 82 - Start 82: cdxmlParserCatchTest - -82: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest -82: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -82: Test timeout computed to be: 1500 -79: [02:22:48] sanitize [02:22:48] UNK: [02:22:48] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -67: Test -67: -67: mrtx1719_3d.mrv -67: -67: Test -67: -67: mrtx1719_atrop1.mrv -67: -67: Test -67: -67: mrtx1719_atrop2.mrv -67: -67: Test -67: -67: mrtx1719_atrop3.mrv -67: -67: Test -67: -67: mrtx1719_atropBad1.mrv -67: -67: [02:22:48] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -79: [02:22:48] skipping block at line 7: 'BEGIN ATOM' +79: [23:09:35] bookmark not found +79: [23:09:35] SGroup 2 is invalid and will be ignored +79: [23:09:35] Explicit valence for atom # 2 O, 3, is greater than permitted +79: [23:09:35] Explicit valence for atom # 1 O, 3, is greater than permitted +79: [23:09:35] Explicit valence for atom # 1 C, 5, is greater than permitted +79: [23:09:35] sanitize [23:09:35] UNK: [23:09:35] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +79: [23:09:35] skipping block at line 7: 'BEGIN ATOM' 79: ATOM 1 CHLO CHL 0 0.000 0.000 0.000 1.00 0.00 CL 79: END 79: -79: [02:22:48] +79: [23:09:35] 79: 79: **** 79: Pre-condition Violation @@ -22475,21 +22552,21 @@ 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::v2::FileParsers::SDMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 3# 0x0000AAAAD095BB80 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 4# 0x0000AAAAD0918F84 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 5# 0x0000AAAAD099C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 6# 0x0000AAAAD099D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 7# 0x0000AAAAD099D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 8# 0x0000AAAAD0970A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x0000AAAAD0970F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000AAAAD08EB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000FFFF949A229C in /lib/aarch64-linux-gnu/libc.so.6 +79: 3# 0x0000AAAABB43BB80 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 4# 0x0000AAAABB3F8F84 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 5# 0x0000AAAABB47C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 6# 0x0000AAAABB47D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 7# 0x0000AAAABB47D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 8# 0x0000AAAABB450A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x0000AAAABB450F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x0000AAAABB3CB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x0000FFFFA09A229C in /lib/aarch64-linux-gnu/libc.so.6 79: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -79: 13# 0x0000AAAAD08EB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x0000AAAABB3CB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [02:22:48] +79: [23:09:35] 79: 79: **** 79: Pre-condition Violation @@ -22501,21 +22578,21 @@ 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::v2::FileParsers::ForwardSDMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 3# 0x0000AAAAD095BB80 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 4# 0x0000AAAAD09190F4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 5# 0x0000AAAAD099C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 6# 0x0000AAAAD099D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 7# 0x0000AAAAD099D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 8# 0x0000AAAAD0970A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x0000AAAAD0970F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000AAAAD08EB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000FFFF949A229C in /lib/aarch64-linux-gnu/libc.so.6 +79: 3# 0x0000AAAABB43BB80 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 4# 0x0000AAAABB3F90F4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 5# 0x0000AAAABB47C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 6# 0x0000AAAABB47D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 7# 0x0000AAAABB47D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 8# 0x0000AAAABB450A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x0000AAAABB450F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x0000AAAABB3CB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x0000FFFFA09A229C in /lib/aarch64-linux-gnu/libc.so.6 79: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -79: 13# 0x0000AAAAD08EB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x0000AAAABB3CB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [02:22:48] +79: [23:09:35] 79: 79: **** 79: Pre-condition Violation @@ -22527,21 +22604,21 @@ 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::v2::FileParsers::SmilesMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 3# 0x0000AAAAD095BB80 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 4# 0x0000AAAAD0919428 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 5# 0x0000AAAAD099C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 6# 0x0000AAAAD099D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 7# 0x0000AAAAD099D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 8# 0x0000AAAAD0970A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x0000AAAAD0970F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000AAAAD08EB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000FFFF949A229C in /lib/aarch64-linux-gnu/libc.so.6 +79: 3# 0x0000AAAABB43BB80 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 4# 0x0000AAAABB3F9428 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 5# 0x0000AAAABB47C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 6# 0x0000AAAABB47D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 7# 0x0000AAAABB47D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 8# 0x0000AAAABB450A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x0000AAAABB450F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x0000AAAABB3CB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x0000FFFFA09A229C in /lib/aarch64-linux-gnu/libc.so.6 79: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -79: 13# 0x0000AAAAD08EB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x0000AAAABB3CB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [02:22:48] +79: [23:09:35] 79: 79: **** 79: Pre-condition Violation @@ -22553,21 +22630,21 @@ 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::v2::FileParsers::TDTMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 3# 0x0000AAAAD095BB80 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 4# 0x0000AAAAD09196C4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 5# 0x0000AAAAD099C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 6# 0x0000AAAAD099D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 7# 0x0000AAAAD099D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 8# 0x0000AAAAD0970A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x0000AAAAD0970F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000AAAAD08EB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000FFFF949A229C in /lib/aarch64-linux-gnu/libc.so.6 +79: 3# 0x0000AAAABB43BB80 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 4# 0x0000AAAABB3F96C4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 5# 0x0000AAAABB47C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 6# 0x0000AAAABB47D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 7# 0x0000AAAABB47D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 8# 0x0000AAAABB450A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x0000AAAABB450F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x0000AAAABB3CB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x0000FFFFA09A229C in /lib/aarch64-linux-gnu/libc.so.6 79: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -79: 13# 0x0000AAAAD08EB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x0000AAAABB3CB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [02:22:48] +79: [23:09:35] 79: 79: **** 79: Pre-condition Violation @@ -22579,29 +22656,29 @@ 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 3# 0x0000AAAAD095BB80 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 4# 0x0000AAAAD09198BC in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 5# 0x0000AAAAD099C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 6# 0x0000AAAAD099D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 7# 0x0000AAAAD099D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 8# 0x0000AAAAD0970A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x0000AAAAD0970F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000AAAAD08EB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000FFFF949A229C in /lib/aarch64-linux-gnu/libc.so.6 +79: 3# 0x0000AAAABB43BB80 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 4# 0x0000AAAABB3F98BC in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 5# 0x0000AAAABB47C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 6# 0x0000AAAABB47D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 7# 0x0000AAAABB47D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 8# 0x0000AAAABB450A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x0000AAAABB450F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x0000AAAABB3CB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x0000FFFFA09A229C in /lib/aarch64-linux-gnu/libc.so.6 79: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -79: 13# 0x0000AAAAD08EB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x0000AAAABB3CB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [02:22:48] Found a SCD/SED line with missing/empty SDT specification at line 21 -79: [02:22:48] Found a SCD/SED line with missing/empty SDT specification at line 20 -79: [02:22:48] BEGIN SGROUP line not found on line 14 -79: [02:22:48] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. -79: [02:22:48] END SGROUP line not found on line 14 -79: [02:22:48] END SGROUP line not found on line 14 -79: [02:22:48] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. -79: [02:22:48] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. -79: [02:22:48] +79: [23:09:35] Found a SCD/SED line with missing/empty SDT specification at line 21 +79: [23:09:35] Found a SCD/SED line with missing/empty SDT specification at line 20 +79: [23:09:35] BEGIN SGROUP line not found on line 14 +79: [23:09:35] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. +79: [23:09:35] END SGROUP line not found on line 14 +79: [23:09:35] END SGROUP line not found on line 14 +79: [23:09:35] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. +79: [23:09:35] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. +79: [23:09:35] 79: 79: **** 79: Range Error @@ -22616,38 +22693,49 @@ 79: 3# RDKit::FileParserUtils::finishMolProcessing(RDKit::RWMol*, bool, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 4# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 5# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 6# 0x0000AAAAD095B7F4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 7# 0x0000AAAAD091E910 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 8# 0x0000AAAAD099C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x0000AAAAD099D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000AAAAD099D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000AAAAD0970A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000AAAAD0970F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000AAAAD08EB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x0000FFFF949A229C in /lib/aarch64-linux-gnu/libc.so.6 +79: 6# 0x0000AAAABB43B7F4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 7# 0x0000AAAABB3FE910 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 8# 0x0000AAAABB47C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x0000AAAABB47D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x0000AAAABB47D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x0000AAAABB450A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x0000AAAABB450F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x0000AAAABB3CB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x0000FFFFA09A229C in /lib/aarch64-linux-gnu/libc.so.6 79: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -79: 16# 0x0000AAAAD08EB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0x0000AAAABB3CB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [02:22:48] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. -79: [02:22:48] Multiple ATTCHPT values for atom 2 on line 9 -79: [02:22:48] Found a SCD/SED line with missing/empty SDT specification at line 12 -79: [02:22:48] SMARTS Parse Error: syntax error while parsing: [#6;R -79: [02:22:48] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' -79: [02:22:48] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. -79: [02:22:48] Skipping empty SMARTS value for SMARTSQ. -79: [02:22:48] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. -79: [02:22:48] Found a SCD/SED line with missing/empty SDT specification at line 12 -79: [02:22:48] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -79: [02:22:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -79: [02:22:48] WARNING: Skipping property bar because the value includes an illegal blank line -79: [02:22:48] WARNING: Skipping property baz because the value includes an illegal blank line -79: [02:22:48] WARNING: Skipping property bletch +79: [23:09:35] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. +79: [23:09:35] Multiple ATTCHPT values for atom 2 on line 9 +79: [23:09:35] Found a SCD/SED line with missing/empty SDT specification at line 12 +79: [23:09:35] SMARTS Parse Error: syntax error while parsing: [#6;R +79: [23:09:35] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' +79: [23:09:35] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. +79: [23:09:35] Skipping empty SMARTS value for SMARTSQ. +79: [23:09:35] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. +79: [23:09:35] Found a SCD/SED line with missing/empty SDT specification at line 12 +79: [23:09:35] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +80: Randomness seeded to: 2018990436 +80: =============================================================================== +80: All tests passed (95 assertions in 4 test cases) +80: + 69/230 Test #80: testPropertyLists ...................... Passed 0.10 sec +test 81 + Start 81: XYZFileParserCatchTest + +81: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/XYZFileParserCatchTest +81: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +81: Test timeout computed to be: 1500 +79: [23:09:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +79: [23:09:35] WARNING: Skipping property bar because the value includes an illegal blank line +79: [23:09:35] WARNING: Skipping property baz because the value includes an illegal blank line +79: [23:09:35] WARNING: Skipping property bletch 79: nope because the name includes a newline -79: [02:22:48] WARNING: Skipping property bletch +79: [23:09:35] WARNING: Skipping property bletch 79: nope2 because the name includes a newline -79: [02:22:48] +79: [23:09:35] 79: 79: **** 79: Post-condition Violation @@ -22659,26 +22747,26 @@ 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 3# 0x0000FFFF952B7CC4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 4# 0x0000FFFF952C7F18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 5# 0x0000FFFF952C8B58 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 3# 0x0000FFFFA12B7CC4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 4# 0x0000FFFFA12C7F18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 5# 0x0000FFFFA12C8B58 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 9# 0x0000AAAAD08F3BD4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000AAAAD099C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000AAAAD099D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000AAAAD099D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000AAAAD0970A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x0000AAAAD0970F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x0000AAAAD08EB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 16# 0x0000FFFF949A229C in /lib/aarch64-linux-gnu/libc.so.6 +79: 9# 0x0000AAAABB3D3BD4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x0000AAAABB47C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x0000AAAABB47D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x0000AAAABB47D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x0000AAAABB450A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x0000AAAABB450F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x0000AAAABB3CB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0x0000FFFFA09A229C in /lib/aarch64-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -79: 18# 0x0000AAAAD08EB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 18# 0x0000AAAABB3CB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [02:22:48] +79: [23:09:35] 79: 79: **** 79: Post-condition Violation @@ -22690,26 +22778,26 @@ 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 3# 0x0000FFFF952B7CC4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 4# 0x0000FFFF952C7F18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 5# 0x0000FFFF952C8B58 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 3# 0x0000FFFFA12B7CC4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 4# 0x0000FFFFA12C7F18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 5# 0x0000FFFFA12C8B58 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 9# 0x0000AAAAD08F34F8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000AAAAD099C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000AAAAD099D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000AAAAD099D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000AAAAD0970A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x0000AAAAD0970F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x0000AAAAD08EB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 16# 0x0000FFFF949A229C in /lib/aarch64-linux-gnu/libc.so.6 +79: 9# 0x0000AAAABB3D34F8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x0000AAAABB47C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x0000AAAABB47D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x0000AAAABB47D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x0000AAAABB450A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x0000AAAABB450F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x0000AAAABB3CB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0x0000FFFFA09A229C in /lib/aarch64-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -79: 18# 0x0000AAAAD08EB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 18# 0x0000AAAABB3CB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [02:22:48] +79: [23:09:35] 79: 79: **** 79: Post-condition Violation @@ -22721,26 +22809,26 @@ 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 3# 0x0000FFFF952B7CC4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 4# 0x0000FFFF952C58A0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 5# 0x0000FFFF952C67CC in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 3# 0x0000FFFFA12B7CC4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 4# 0x0000FFFFA12C58A0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 5# 0x0000FFFFA12C67CC in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 9# 0x0000AAAAD08F3B90 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000AAAAD099C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000AAAAD099D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000AAAAD099D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000AAAAD0970A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x0000AAAAD0970F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x0000AAAAD08EB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 16# 0x0000FFFF949A229C in /lib/aarch64-linux-gnu/libc.so.6 +79: 9# 0x0000AAAABB3D3B90 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x0000AAAABB47C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x0000AAAABB47D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x0000AAAABB47D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x0000AAAABB450A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x0000AAAABB450F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x0000AAAABB3CB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0x0000FFFFA09A229C in /lib/aarch64-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -79: 18# 0x0000AAAAD08EB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 18# 0x0000AAAABB3CB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [02:22:48] +79: [23:09:35] 79: 79: **** 79: Post-condition Violation @@ -22752,75 +22840,51 @@ 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 3# 0x0000FFFF952B7CC4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 4# 0x0000FFFF952C58A0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 5# 0x0000FFFF952C67CC in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 3# 0x0000FFFFA12B7CC4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 4# 0x0000FFFFA12C58A0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 5# 0x0000FFFFA12C67CC in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 9# 0x0000AAAAD08F38C8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000AAAAD099C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000AAAAD099D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000AAAAD099D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 13# 0x0000AAAAD0970A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 14# 0x0000AAAAD0970F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 15# 0x0000AAAAD08EB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 16# 0x0000FFFF949A229C in /lib/aarch64-linux-gnu/libc.so.6 +79: 9# 0x0000AAAABB3D38C8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x0000AAAABB47C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x0000AAAABB47D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x0000AAAABB47D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x0000AAAABB450A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x0000AAAABB450F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 15# 0x0000AAAABB3CB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 16# 0x0000FFFFA09A229C in /lib/aarch64-linux-gnu/libc.so.6 79: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -79: 18# 0x0000AAAAD08EB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 18# 0x0000AAAABB3CB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [02:22:48] atom 3 has a negative isotope value. line: 15 -67: Test -67: -67: AlexRxn.mrv -67: -67: Test -67: -67: BadReactionSign.mrv -67: -67: Test -67: -67: bondArray_node.mrv -67: -67: Test -67: -67: marvin03.mrv -67: -67: Test -67: -67: marvin04.mrv -67: -67: Test -67: -67: marvin08.mrv -67: -67: Test -67: -67: marvin09.mrv -67: -67: Test -67: -67: marvin11.mrv -67: -67: Test -67: -67: marvin05.mrv -67: -67: Test -67: -67: EmptyRxn.mrv -67: -67: [02:22:48] initialization failed -82: Randomness seeded to: 4096848337 -82: [02:22:48] Invalid or missing fragment id from CDXML fragment, assigning new one... -82: [02:22:48] Explicit valence for atom # 3 N, 4, is greater than permitted -82: [02:22:48] CDXMLParser: failed sanitizing skipping fragment 32 -82: [02:22:48] Bad bond in CDXML skipping fragment 58... -82: [02:22:48] Invalid or missing fragment id from CDXML fragment, assigning new one... -82: [02:22:48] Bad bond in CDXML skipping fragment 58... -79: [02:22:48] +79: [23:09:35] atom 3 has a negative isotope value. line: 15 +68: ---------------------------------- +68: ---------------------------------- +68: [23:09:35] +68: +68: **** +68: Pre-condition Violation +68: rlabel out of range for MDL files +68: Violation occurred on line 857 in file ./Code/GraphMol/Atom.cpp +68: Failed Expression: rlabel >= 0 && rlabel < 100 +68: ---------- +68: Stacktrace: +68: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +68: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +68: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +68: 3# 0x0000AAAACAE0EC20 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 4# 0x0000AAAACAE744C4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 5# 0x0000AAAACADE5578 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 6# 0x0000FFFF9509229C in /lib/aarch64-linux-gnu/libc.so.6 +68: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +68: 8# 0x0000AAAACADE57B0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: ---------- +68: **** +68: +68: [23:09:35] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +79: [23:09:35] 79: 79: **** 79: Invariant Violation @@ -22831,23 +22895,23 @@ 79: Stacktrace: 79: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -79: 2# 0x0000FFFF953879D8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +79: 2# 0x0000FFFFA13879D8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 3# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 4# 0x0000AAAAD095BB80 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 5# 0x0000AAAAD092FCA0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 6# 0x0000AAAAD099C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 7# 0x0000AAAAD099D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 8# 0x0000AAAAD099D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x0000AAAAD0970A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000AAAAD0970F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000AAAAD08EB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 12# 0x0000FFFF949A229C in /lib/aarch64-linux-gnu/libc.so.6 +79: 4# 0x0000AAAABB43BB80 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 5# 0x0000AAAABB40FCA0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 6# 0x0000AAAABB47C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 7# 0x0000AAAABB47D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 8# 0x0000AAAABB47D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x0000AAAABB450A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x0000AAAABB450F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x0000AAAABB3CB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 12# 0x0000FFFFA09A229C in /lib/aarch64-linux-gnu/libc.so.6 79: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -79: 14# 0x0000AAAAD08EB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 14# 0x0000AAAABB3CB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -79: [02:22:48] +79: [23:09:35] 79: 79: **** 79: Pre-condition Violation @@ -22860,215 +22924,154 @@ 79: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 79: 2# RDKit::v2::FileParsers::MaeMolSupplier::init() in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 79: 3# RDKit::v2::FileParsers::MaeMolSupplier::reset() in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -79: 4# 0x0000AAAAD092FFC4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 5# 0x0000AAAAD099C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 6# 0x0000AAAAD099D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 7# 0x0000AAAAD099D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 8# 0x0000AAAAD0970A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 9# 0x0000AAAAD0970F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 10# 0x0000AAAAD08EB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -79: 11# 0x0000FFFF949A229C in /lib/aarch64-linux-gnu/libc.so.6 +79: 4# 0x0000AAAABB40FFC4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 5# 0x0000AAAABB47C64C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 6# 0x0000AAAABB47D000 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 7# 0x0000AAAABB47D434 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 8# 0x0000AAAABB450A18 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 9# 0x0000AAAABB450F64 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 10# 0x0000AAAABB3CB730 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 11# 0x0000FFFFA09A229C in /lib/aarch64-linux-gnu/libc.so.6 79: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -79: 13# 0x0000AAAAD08EB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +79: 13# 0x0000AAAABB3CB7F0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 79: ---------- 79: **** 79: -67: Test -67: -67: RxnNoCoords.mrv -67: -67: Test -67: -67: mrvValenceZero.mrv -67: -67: Test -67: -67: condition_coordinates_mpoint.mrv -67: -67: Test -67: -67: marvin01.mrv -67: -67: Test -67: -67: aspirineSynthesisWithAttributes.mrv -67: -67: Test -67: -67: marvin01.mrv -67: -67: Test -67: -67: NewChiralTest -67: -67: Test -67: -67: NewChiralTest -67: -67: Test -67: -67: NewChiralTestNoChiral -67: -67: Test -67: -67: NewChiralTestNoChiral -67: -67: Test -67: -67: NewChiralTest2 -67: -67: Test -67: -67: NewChiralTest2 -67: -67: Test -67: -67: NewChiralTest2AllChiral -67: -67: Test -67: -67: NewChiralTest2AllChiral -67: -67: Test -67: -67: Vendor839 -67: -67: Test -67: -67: DoubleBondChain -67: -67: Test -67: -67: Na_Mg_Al_OH -67: -67: Test -67: -67: Pb -67: -67: Test -67: -67: O_Mg_Si -67: -67: Test -67: -67: SquiggleBond -67: -67: Test -67: -67: BigMacrocycle -67: -67: Test -67: -67: Smiles1 -67: - 71/230 Test #67: testMrvToMol ........................... Passed 1.67 sec +81: Randomness seeded to: 1645583409 +81: =============================================================================== +81: All tests passed (100 assertions in 2 test cases) +81: + 70/230 Test #81: XYZFileParserCatchTest ................. Passed 0.08 sec +test 82 + Start 82: cdxmlParserCatchTest + +82: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest +82: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +82: Test timeout computed to be: 1500 +79: [23:09:35] ERROR: molecules without atoms cannot be exported to Maestro files. +79: [23:09:35] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +79: [23:09:35] ERROR: the mol cannot be kekulized, and will not be written to the output file. +79: [23:09:35] ERROR: Bond 0 has a type that is not supported by maeparser. The mol will not be written to the output file. +79: [23:09:35] WARNING: atom 1 in input Maestro file has atomic number '0', which is reserved for internal use, and not allowed in inputs. The atom will be ignored.[23:09:35] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +79: [23:09:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +79: [23:09:35] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +79: [23:09:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +82: Randomness seeded to: 4176546191 +82: [23:09:35] Invalid or missing fragment id from CDXML fragment, assigning new one... +82: [23:09:35] Explicit valence for atom # 3 N, 4, is greater than permitted +82: [23:09:35] CDXMLParser: failed sanitizing skipping fragment 32 +82: [23:09:35] Bad bond in CDXML skipping fragment 58... +82: [23:09:35] Invalid or missing fragment id from CDXML fragment, assigning new one... +82: [23:09:35] Bad bond in CDXML skipping fragment 58... +82: [23:09:35] WARNING: not removing hydrogen atom without neighbors +82: [23:09:35] WARNING: not removing hydrogen atom without neighbors +82: [23:09:35] WARNING: not removing hydrogen atom without neighbors +82: [23:09:35] WARNING: not removing hydrogen atom without neighbors +82: [23:09:35] WARNING: not removing hydrogen atom without neighbors +82: [23:09:35] WARNING: not removing hydrogen atom without neighbors +82: [23:09:35] WARNING: not removing hydrogen atom without neighbors +82: [23:09:35] WARNING: not removing hydrogen atom without neighbors +82: [23:09:35] WARNING: not removing hydrogen atom without neighbors +82: [23:09:35] WARNING: not removing hydrogen atom without neighbors +82: [23:09:35] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents reaction fragment 64603 not found in document. +82: [23:09:35] Incomplete atom labelling, cannot make bond +82: [23:09:35] Incomplete atom labelling, cannot make bond +82: [23:09:35] Incomplete atom labelling, cannot make bond +82: [23:09:36] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +82: [23:09:36] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +82: [23:09:36] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast +82: [23:09:36] Failed to parse XML fragment 5 node: b attribute: Order: 5 +82: [23:09:36] Invalid or missing fragment id from CDXML fragment, assigning new one... +82: =============================================================================== +82: All tests passed (263 assertions in 7 test cases) +82: + 71/230 Test #82: cdxmlParserCatchTest ................... Passed 0.37 sec test 83 Start 83: molfileStereoCatchTest 83: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/molfileStereoCatchTest 83: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 83: Test timeout computed to be: 1500 -82: [02:22:48] WARNING: not removing hydrogen atom without neighbors -82: [02:22:48] WARNING: not removing hydrogen atom without neighbors -82: [02:22:48] WARNING: not removing hydrogen atom without neighbors -68: [02:22:48] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -68: [02:22:48] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -79: [02:22:48] ERROR: molecules without atoms cannot be exported to Maestro files. -79: [02:22:48] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -79: [02:22:48] ERROR: the mol cannot be kekulized, and will not be written to the output file. -79: [02:22:48] ERROR: Bond 0 has a type that is not supported by maeparser. The mol will not be written to the output file. -82: [02:22:48] WARNING: not removing hydrogen atom without neighbors -82: [02:22:48] WARNING: not removing hydrogen atom without neighbors -82: [02:22:48] WARNING: not removing hydrogen atom without neighbors -82: [02:22:48] WARNING: not removing hydrogen atom without neighbors -82: [02:22:48] WARNING: not removing hydrogen atom without neighbors -82: [02:22:48] WARNING: not removing hydrogen atom without neighbors -79: [02:22:48] WARNING: atom 1 in input Maestro file has atomic number '0', which is reserved for internal use, and not allowed in inputs. The atom will be ignored.[02:22:48] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -79: [02:22:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -79: [02:22:48] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -79: [02:22:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -83: Randomness seeded to: 4275538103 -83: [02:22:48] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -83: [02:22:48] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -83: [02:22:48] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -83: [02:22:48] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +83: Randomness seeded to: 1494154635 +83: [23:09:36] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +83: [23:09:36] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +83: [23:09:36] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +83: [23:09:36] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. 83: =============================================================================== 83: All tests passed (142 assertions in 6 test cases) 83: -82: [02:22:48] WARNING: not removing hydrogen atom without neighbors -82: [02:22:48] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents reaction fragment 64603 not found in document. - 72/230 Test #83: molfileStereoCatchTest ................. Passed 0.04 sec + 72/230 Test #83: molfileStereoCatchTest ................. Passed 0.10 sec test 84 Start 84: connectTheDotsTest 84: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/connectTheDotsTest 84: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 84: Test timeout computed to be: 1500 -84: Randomness seeded to: 1684202947 +84: Randomness seeded to: 3991386673 84: =============================================================================== 84: All tests passed (8 assertions in 1 test case) 84: -82: [02:22:48] Incomplete atom labelling, cannot make bond -82: [02:22:48] Incomplete atom labelling, cannot make bond - 73/230 Test #84: connectTheDotsTest ..................... Passed 0.04 sec +68: [23:09:36] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +68: [23:09:36] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' + 73/230 Test #84: connectTheDotsTest ..................... Passed 0.07 sec test 85 Start 85: v2MolSuppliers 85: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/v2MolSuppliers 85: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 85: Test timeout computed to be: 1500 -68: [02:22:48] Empty atom list: 'M ALS 1 0 F' on line 8. -82: [02:22:48] Incomplete atom labelling, cannot make bond -39: [02:22:48] Finished -39: [02:22:48] testing stability w.r.t. renumbering. -85: Randomness seeded to: 3170178307 +85: Randomness seeded to: 4147445579 85: =============================================================================== 85: All tests passed (12 assertions in 5 test cases) 85: - 74/230 Test #85: v2MolSuppliers ......................... Passed 0.05 sec + 74/230 Test #85: v2MolSuppliers ......................... Passed 0.08 sec test 86 Start 86: v2FileParsersCatchTest 86: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/v2FileParsersCatchTest 86: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 86: Test timeout computed to be: 1500 -39: [02:22:48] Finished -39: [02:22:48] testing smiles round-tripping. -82: [02:22:48] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -82: [02:22:48] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -82: [02:22:48] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast -82: [02:22:48] Failed to parse XML fragment 5 node: b attribute: Order: 5 -82: [02:22:48] Invalid or missing fragment id from CDXML fragment, assigning new one... -82: =============================================================================== -82: All tests passed (263 assertions in 7 test cases) -82: +68: [23:09:36] Empty atom list: 'M ALS 1 0 F' on line 8. 68: de_DE.UTF-8 -68: [02:22:48] ------------------------------------- -68: [02:22:48] Test multithreading Locale Switching - 75/230 Test #82: cdxmlParserCatchTest ................... Passed 0.31 sec +68: [23:09:36] ------------------------------------- +68: [23:09:36] Test multithreading Locale Switching +12: .................. +12: ---------------------------------------------------------------------- +12: Ran 18 tests in 6.247s +12: +12: OK +86: Randomness seeded to: 370425793 +86: =============================================================================== +86: All tests passed (6 assertions in 1 test case) +86: +68: [23:09:36] Test multithreading (Done) +68: [23:09:36] ------------------------------------- + 75/230 Test #86: v2FileParsersCatchTest ................. Passed 0.09 sec test 87 Start 87: multithreadedSupplierCatchTest 87: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/multithreadedSupplierCatchTest 87: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 87: Test timeout computed to be: 1500 -68: [02:22:48] Test multithreading (Done) -68: [02:22:48] ------------------------------------- -86: Randomness seeded to: 1502250663 -86: =============================================================================== -86: All tests passed (6 assertions in 1 test case) -86: - 76/230 Test #86: v2FileParsersCatchTest ................. Passed 0.05 sec +68: *************************************** +68: *************************************** +68: [23:09:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: [23:09:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: [23:09:36] bond with order 0 found on line 7. This is not part of the MDL specification. +68: [23:09:36] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +68: [23:09:36] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +68: [23:09:36] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +68: generating smiles +68: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 +68: converting back +68: check isomorphism + 76/230 Test #12: pyBV ................................... Passed 7.39 sec test 88 Start 88: testSubstructMatch 88: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 88: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Substruct 88: Test timeout computed to be: 1500 -68: *************************************** -68: *************************************** -68: [02:22:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: [02:22:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 88: ----------------- Test 1 88: Done 88: @@ -23093,33 +23096,15 @@ 88: ----------------- Testing serial numbers on recursive queries 88: Done 88: -88: [02:22:48] ------------------------------------- -88: [02:22:48] Test multithreading +88: [23:09:36] ------------------------------------- +88: [23:09:36] Test multithreading 88: reading molecules -68: [02:22:48] bond with order 0 found on line 7. This is not part of the MDL specification. -68: [02:22:48] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -68: [02:22:48] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -68: [02:22:48] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -68: generating smiles -68: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 -68: converting back 88: hits: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 88: processing 88: launch :0 88: launch :1 88: launch :2 88: launch :3 -68: check isomorphism -39: [02:22:48] Finished -39: [02:22:48] testing github #1567: Non-canonical result from MolFragmentToSmiles() -39: [02:22:48] Finished - 77/230 Test #39: hanoiTest .............................. Passed 3.02 sec -test 89 - Start 89: substructTestCatch - -89: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/substructTestCatch -89: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Substruct -89: Test timeout computed to be: 1500 88: done 88: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 88: processing2 @@ -23135,35 +23120,52 @@ 88: launch3 :1 88: launch3 :2 88: launch3 :3 +39: [23:09:36] done: 500000 +39: [23:09:36] Done +39: [23:09:37] Testing hanoi with a functor. +39: [23:09:37] Done +39: [23:09:37] Testing basic partition refinement. +39: [23:09:37] Done +39: [23:09:37] Testing partition refinement with neighbors. +39: [23:09:37] Done +39: [23:09:37] testing canonicalization via tie breaking. +39: [23:09:37] Done +39: [23:09:37] testing canonicalization using the wrapper. 88: done -88: [02:22:49] done -88: [02:22:49] ------------------------------------- -88: [02:22:49] Test GitHub issue 15 -88: [02:22:49] done -88: [02:22:49] ------------------------------------- -88: [02:22:49] Test GitHub issue 409 -88: [02:22:49] done -88: [02:22:49] ------------------------------------- -88: [02:22:49] Test chiral matching -88: [02:22:49] done -88: [02:22:49] ------------------------------------- -88: [02:22:49] Test GitHub issue 688: partially specified chiral substructure queries don't work properly -88: [02:22:49] done -88: [02:22:49] ------------------------------------- -88: [02:22:49] Test dative-bond matching -88: [02:22:49] done -88: [02:22:49] ------------------------------------- -88: [02:22:49] Test cis/trans matching -88: [02:22:49] done -88: [02:22:49] ------------------------------------- -88: [02:22:49] Test cis/trans matching part 2 -88: [02:22:49] done -88: [02:22:49] ------------------------------------- -88: [02:22:49] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS -88: [02:22:49] done -88: [02:22:49] ------------------------------------- -88: [02:22:49] Testing matching E/Z against Cis/Trans stereo bonds -88: [02:22:49] +88: [23:09:37] done +88: [23:09:37] ------------------------------------- +88: [23:09:37] Test GitHub issue 15 +88: [23:09:37] done +88: [23:09:37] ------------------------------------- +88: [23:09:37] Test GitHub issue 409 +88: [23:09:37] done +88: [23:09:37] ------------------------------------- +88: [23:09:37] Test chiral matching +88: [23:09:37] done +88: [23:09:37] ------------------------------------- +88: [23:09:37] Test GitHub issue 688: partially specified chiral substructure queries don't work properly +88: [23:09:37] done +88: [23:09:37] ------------------------------------- +88: [23:09:37] Test dative-bond matching +88: [23:09:37] done +88: [23:09:37] ------------------------------------- +88: [23:09:37] Test cis/trans matching +88: [23:09:37] done +88: [23:09:37] ------------------------------------- +88: [23:09:37] Test cis/trans matching part 2 +88: [23:09:37] done +88: [23:09:37] ------------------------------------- +88: [23:09:37] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS +88: [23:09:37] done +88: [23:09:37] ------------------------------------- +88: [23:09:37] Testing matching E/Z against Cis/Trans stereo bonds +39: [23:09:37] Done +39: [23:09:37] testing some specific ordering problems +39: [23:09:37] Finished +39: [23:09:37] testing chiral invariants. +39: [23:09:37] Finished +39: [23:09:37] testing unique ranks in w.r.t. renumbering. +88: [23:09:37] 88: 88: **** 88: Pre-condition Violation @@ -23176,15 +23178,15 @@ 88: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 88: 2# RDKit::detail::ScoreMatchesByDegreeOfCoreSubstitution::ScoreMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 88: 3# RDKit::getMostSubstitutedCoreMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -88: 4# 0x0000AAAAB1AEBEE4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -88: 5# 0x0000AAAAB1AE9728 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -88: 6# 0x0000FFFFAB5E229C in /lib/aarch64-linux-gnu/libc.so.6 +88: 4# 0x0000AAAAC703BEE4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +88: 5# 0x0000AAAAC7039728 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +88: 6# 0x0000FFFFBDC5229C in /lib/aarch64-linux-gnu/libc.so.6 88: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -88: 8# 0x0000AAAAB1AE9930 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +88: 8# 0x0000AAAAC7039930 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 88: ---------- 88: **** 88: -88: [02:22:49] +88: [23:09:37] 88: 88: **** 88: Pre-condition Violation @@ -23197,37 +23199,69 @@ 88: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 88: 2# RDKit::detail::ScoreMatchesByDegreeOfCoreSubstitution::ScoreMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 88: 3# RDKit::sortMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -88: 4# 0x0000AAAAB1AEC324 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -88: 5# 0x0000AAAAB1AE9728 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -88: 6# 0x0000FFFFAB5E229C in /lib/aarch64-linux-gnu/libc.so.6 +88: 4# 0x0000AAAAC703C324 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +88: 5# 0x0000AAAAC7039728 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +88: 6# 0x0000FFFFBDC5229C in /lib/aarch64-linux-gnu/libc.so.6 88: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -88: 8# 0x0000AAAAB1AE9930 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +88: 8# 0x0000AAAAC7039930 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 88: ---------- 88: **** 88: -88: [02:22:49] ------------------------------------- -88: [02:22:49] Test substructure matching with a pathological case for symmetric SSSR -88: [02:22:49] ------------------------------------- -88: [02:22:49] Test isAtomTerminalRGroupOrQueryHydrogen - 78/230 Test #88: testSubstructMatch ..................... Passed 0.31 sec +88: [23:09:37] ------------------------------------- +88: [23:09:37] Test substructure matching with a pathological case for symmetric SSSR +88: [23:09:37] ------------------------------------- +88: [23:09:37] Test isAtomTerminalRGroupOrQueryHydrogen + 77/230 Test #88: testSubstructMatch ..................... Passed 0.58 sec +test 89 + Start 89: substructTestCatch + +89: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/substructTestCatch +89: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Substruct +89: Test timeout computed to be: 1500 +39: [23:09:37] Finished +39: [23:09:37] testing mol fragments. +39: [23:09:37] Finished +39: [23:09:37] testing protein round-tripping. +27: All 191 tests passed +87: Randomness seeded to: 433629771 +87: [23:09:37] Explicit valence for atom # 9 N, 6, is greater than permitted +89: Randomness seeded to: 1886079332 +89: =============================================================================== +89: All tests passed (197 assertions in 9 test cases) +89: + 78/230 Test #89: substructTestCatch ..................... Passed 0.82 sec test 90 Start 90: testGenericGroups 90: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups/testGenericGroups 90: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups 90: Test timeout computed to be: 1500 -12: .................. -12: ---------------------------------------------------------------------- -12: Ran 18 tests in 3.694s -12: -12: OK -68: [02:22:49] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -68: [02:22:49] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -68: [02:22:49] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -68: [02:22:49] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -68: [02:22:49] deprecated group abbreviation ignored on line 24 +27: +27: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... +87: [23:09:38] Explicit valence for atom # 3 Al, 6, is greater than permitted +39: [23:09:38] Finished +39: [23:09:38] testing stability w.r.t. renumbering. +39: [23:09:38] Finished +39: [23:09:38] testing smiles round-tripping. +87: [23:09:38] Explicit valence for atom # 4 Al, 6, is greater than permitted +87: [23:09:38] Explicit valence for atom # 10 Si, 6, is greater than permitted +39: [23:09:38] Finished +39: [23:09:38] testing github #1567: Non-canonical result from MolFragmentToSmiles() +39: [23:09:38] Finished + 79/230 Test #39: hanoiTest .............................. Passed 7.56 sec +test 91 + Start 91: testReaction + +91: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/testReaction +91: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions +91: Test timeout computed to be: 1500 +68: [23:09:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +68: [23:09:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +68: [23:09:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +68: [23:09:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +68: [23:09:38] deprecated group abbreviation ignored on line 24 68: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] -68: [02:22:49] +68: [23:09:38] 68: 68: **** 68: Post-condition Violation @@ -23239,314 +23273,222 @@ 68: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 68: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 68: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -68: 3# 0x0000FFFF805A7CC4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -68: 4# 0x0000FFFF805B58A0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -68: 5# 0x0000FFFF805B67CC in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +68: 3# 0x0000FFFF959B7CC4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +68: 4# 0x0000FFFF959C58A0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +68: 5# 0x0000FFFF959C67CC in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 68: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 68: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 68: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -68: 9# 0x0000AAAAC6F2F15C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: 10# 0x0000AAAAC6FA4464 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: 11# 0x0000AAAAC6F155EC in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: 12# 0x0000FFFF7FC8229C in /lib/aarch64-linux-gnu/libc.so.6 +68: 9# 0x0000AAAACADFF15C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 10# 0x0000AAAACAE74464 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 11# 0x0000AAAACADE55EC in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 12# 0x0000FFFF9509229C in /lib/aarch64-linux-gnu/libc.so.6 68: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -68: 14# 0x0000AAAAC6F157B0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 14# 0x0000AAAACADE57B0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 68: ---------- 68: **** 68: - 79/230 Test #12: pyBV ................................... Passed 4.17 sec -test 91 - Start 91: testReaction - -91: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/testReaction -91: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions -91: Test timeout computed to be: 1500 -89: Randomness seeded to: 3368125439 -89: =============================================================================== -89: All tests passed (197 assertions in 9 test cases) -89: - 80/230 Test #89: substructTestCatch ..................... Passed 0.53 sec -test 92 - Start 92: testReactionFingerprints - -92: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/testReactionFingerprints -92: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions -92: Test timeout computed to be: 1500 91: smi: O=C1CNC(=O)CN1 -90: Randomness seeded to: 1892695182 -90: =============================================================================== -90: All tests passed (11480 assertions in 38 test cases) -90: - 81/230 Test #90: testGenericGroups ...................... Passed 0.36 sec -test 93 - Start 93: testEnumeration - -93: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/testEnumeration -93: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions -93: Test timeout computed to be: 1500 91: 1: O=C1CNC(=O)CN1 91: 2: COOC -91: [02:22:49] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -91: [02:22:49] SMARTS Parse Error: Failed parsing SMARTS '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' +91: [23:09:38] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +91: [23:09:38] SMARTS Parse Error: Failed parsing SMARTS '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' 91: O=C1CNC(=O)CN1 -91: [02:22:49] product atom-mapping number 1 found multiple times. -91: [02:22:49] mapped atoms in the reactants were not mapped in the products. +91: [23:09:38] product atom-mapping number 1 found multiple times. +91: [23:09:38] mapped atoms in the reactants were not mapped in the products. 91: unmapped numbers are: 4 -92: [02:22:49] ------------------------------------- -92: [02:22:49] Test Reaction StructuralFingerprint -91: [02:22:49] atom 0 in product 0 has multiple charge specifications. +91: [23:09:38] atom 0 in product 0 has multiple charge specifications. 91: mass: 15.0001 91: Oc1ccccn1 91: Oc1ccc[nH]1 -92: [02:22:49] DEPRECATION WARNING: please use AtomPairGenerator -92: [02:22:49] DEPRECATION WARNING: please use AtomPairGenerator -92: [02:22:49] DEPRECATION WARNING: please use AtomPairGenerator -92: [02:22:49] DEPRECATION WARNING: please use AtomPairGenerator -92: [02:22:49] DEPRECATION WARNING: please use AtomPairGenerator -92: [02:22:49] DEPRECATION WARNING: please use AtomPairGenerator -92: [02:22:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator -92: [02:22:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator -92: [02:22:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator -92: [02:22:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator -92: [02:22:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator -92: [02:22:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator -92: [02:22:49] ------------------------------------- -92: [02:22:49] Test Reaction DifferenceFingerprint -92: [02:22:49] DEPRECATION WARNING: please use AtomPairGenerator -92: [02:22:49] DEPRECATION WARNING: please use AtomPairGenerator -92: [02:22:49] DEPRECATION WARNING: please use AtomPairGenerator -92: [02:22:49] DEPRECATION WARNING: please use AtomPairGenerator -92: [02:22:49] DEPRECATION WARNING: please use AtomPairGenerator -92: [02:22:49] DEPRECATION WARNING: please use AtomPairGenerator -92: [02:22:49] DEPRECATION WARNING: please use AtomPairGenerator -92: [02:22:49] DEPRECATION WARNING: please use AtomPairGenerator -92: [02:22:49] DEPRECATION WARNING: please use AtomPairGenerator -92: [02:22:49] DEPRECATION WARNING: please use AtomPairGenerator -92: [02:22:49] DEPRECATION WARNING: please use AtomPairGenerator -92: [02:22:49] DEPRECATION WARNING: please use AtomPairGenerator -92: [02:22:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator -92: [02:22:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator -92: [02:22:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator -92: [02:22:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator -91: [02:22:49] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] -91: [02:22:49] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' -91: [02:22:49] SMARTS Parse Error: syntax error while parsing: ([C:2] -91: [02:22:49] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -91: [02:22:49] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] -91: [02:22:49] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' -91: [02:22:49] SMARTS Parse Error: syntax error while parsing: [C:2]) -91: [02:22:49] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' -91: [02:22:49] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -91: [02:22:49] SMILES Parse Error: Failed parsing SMILES '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' -91: [02:22:49] reactant 2 has no mapped atoms. - 82/230 Test #92: testReactionFingerprints ............... Passed 0.06 sec -test 94 - Start 94: rxnTestCatch - -94: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/rxnTestCatch -94: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions -94: Test timeout computed to be: 1500 -91: [02:22:49] >> Atoms within one molecule have different RXN roles. -91: [02:22:49] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. -91: [02:22:49] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] -91: [02:22:49] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' -91: [02:22:49] SMARTS Parse Error: syntax error while parsing: ([C:2] -91: [02:22:49] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -91: [02:22:49] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) -91: [02:22:49] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' -91: [02:22:49] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] -91: [02:22:49] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' -91: [02:22:49] reactant 0 has no mapped atoms. -91: [02:22:49] reactant 1 has no mapped atoms. -91: [02:22:49] reactant 3 has no mapped atoms. -91: [02:22:49] product atom-mapping number 2 found multiple times. -91: [02:22:49] product atom-mapping number 3 found multiple times. -91: [02:22:49] product atom-mapping number 4 found multiple times. -91: [02:22:49] product atom-mapping number 5 found multiple times. -91: [02:22:49] product atom-mapping number 6 found multiple times. -91: [02:22:49] product atom-mapping number 7 found multiple times. -91: [02:22:49] product atom-mapping number 8 found multiple times. -91: [02:22:49] product atom-mapping number 12 found multiple times. -91: [02:22:49] product atom-mapping number 9 found multiple times. -91: [02:22:49] product atom-mapping number 10 found multiple times. -91: [02:22:49] product atom-mapping number 11 found multiple times. -91: [02:22:49] reactant 0 has no mapped atoms. -91: [02:22:49] reactant 1 has no mapped atoms. -91: [02:22:49] reactant 3 has no mapped atoms. -91: [02:22:49] reactant atom-mapping number 19 found multiple times. -91: [02:22:49] reactant atom-mapping number 25 found multiple times. -91: [02:22:49] reactant atom-mapping number 20 found multiple times. -91: [02:22:49] reactant atom-mapping number 21 found multiple times. -91: [02:22:49] reactant atom-mapping number 22 found multiple times. -91: [02:22:49] reactant atom-mapping number 23 found multiple times. -91: [02:22:49] reactant atom-mapping number 24 found multiple times. -91: [02:22:49] product atom-mapping number 1 found multiple times. -91: [02:22:49] product atom-mapping number 1 found multiple times. -91: [02:22:49] product atom-mapping number 1 found multiple times. -91: [02:22:49] product atom-mapping number 1 found multiple times. -91: [02:22:49] product atom-mapping number 2 found multiple times. -91: [02:22:49] product atom-mapping number 1 found multiple times. -91: [02:22:49] product atom-mapping number 2 found multiple times. -91: [02:22:49] product atom-mapping number 1 found multiple times. -91: [02:22:49] product atom-mapping number 2 found multiple times. -91: [02:22:49] product atom-mapping number 1 found multiple times. -91: [02:22:49] product atom-mapping number 2 found multiple times. -91: [02:22:49] product atom-mapping number 1 found multiple times. +91: [23:09:38] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] +91: [23:09:38] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' +91: [23:09:38] SMARTS Parse Error: syntax error while parsing: ([C:2] +91: [23:09:38] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +91: [23:09:38] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] +91: [23:09:38] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' +91: [23:09:38] SMARTS Parse Error: syntax error while parsing: [C:2]) +91: [23:09:38] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' +91: [23:09:38] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +91: [23:09:38] SMILES Parse Error: Failed parsing SMILES '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' +91: [23:09:38] reactant 2 has no mapped atoms. +91: [23:09:38] >> Atoms within one molecule have different RXN roles. +91: [23:09:38] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. +91: [23:09:38] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] +91: [23:09:38] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' +91: [23:09:38] SMARTS Parse Error: syntax error while parsing: ([C:2] +91: [23:09:38] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +91: [23:09:38] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) +91: [23:09:38] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' +91: [23:09:38] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] +91: [23:09:38] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' +91: [23:09:38] reactant 0 has no mapped atoms. +91: [23:09:38] reactant 1 has no mapped atoms. +91: [23:09:38] reactant 3 has no mapped atoms. +91: [23:09:38] product atom-mapping number 2 found multiple times. +91: [23:09:38] product atom-mapping number 3 found multiple times. +91: [23:09:38] product atom-mapping number 4 found multiple times. +91: [23:09:38] product atom-mapping number 5 found multiple times. +91: [23:09:38] product atom-mapping number 6 found multiple times. +91: [23:09:38] product atom-mapping number 7 found multiple times. +91: [23:09:38] product atom-mapping number 8 found multiple times. +91: [23:09:38] product atom-mapping number 12 found multiple times. +91: [23:09:38] product atom-mapping number 9 found multiple times. +91: [23:09:38] product atom-mapping number 10 found multiple times. +91: [23:09:38] product atom-mapping number 11 found multiple times. +91: [23:09:38] reactant 0 has no mapped atoms. +91: [23:09:38] reactant 1 has no mapped atoms. +91: [23:09:38] reactant 3 has no mapped atoms. +91: [23:09:38] reactant atom-mapping number 19 found multiple times. +91: [23:09:38] reactant atom-mapping number 25 found multiple times. +91: [23:09:38] reactant atom-mapping number 20 found multiple times. +91: [23:09:38] reactant atom-mapping number 21 found multiple times. +91: [23:09:38] reactant atom-mapping number 22 found multiple times. +91: [23:09:38] reactant atom-mapping number 23 found multiple times. +91: [23:09:38] reactant atom-mapping number 24 found multiple times. +91: [23:09:38] product atom-mapping number 1 found multiple times. +91: [23:09:38] product atom-mapping number 1 found multiple times. +91: [23:09:38] product atom-mapping number 1 found multiple times. +91: [23:09:38] product atom-mapping number 1 found multiple times. +91: [23:09:38] product atom-mapping number 2 found multiple times. +91: [23:09:38] product atom-mapping number 1 found multiple times. +91: [23:09:38] product atom-mapping number 2 found multiple times. +91: [23:09:38] product atom-mapping number 1 found multiple times. +91: [23:09:38] product atom-mapping number 2 found multiple times. +91: [23:09:38] product atom-mapping number 1 found multiple times. +91: [23:09:38] product atom-mapping number 2 found multiple times. +91: [23:09:38] product atom-mapping number 1 found multiple times. 91: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -91: [02:22:49] product atom-mapping number 2 found multiple times. -91: [02:22:49] product atom-mapping number 1 found multiple times. -91: [02:22:49] product atom-mapping number 2 found multiple times. -91: [02:22:49] product atom-mapping number 1 found multiple times. +91: [23:09:38] product atom-mapping number 2 found multiple times. +91: [23:09:38] product atom-mapping number 1 found multiple times. +91: [23:09:38] product atom-mapping number 2 found multiple times. +91: [23:09:38] product atom-mapping number 1 found multiple times. 91: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -91: [02:22:49] product atom-mapping number 5 found multiple times. -91: [02:22:49] product atom-mapping number 2 found multiple times. -91: [02:22:49] product atom-mapping number 3 found multiple times. -91: [02:22:49] product atom-mapping number 1 found multiple times. -91: [02:22:49] product atom-mapping number 4 found multiple times. -91: [02:22:49] product atom-mapping number 5 found multiple times. -91: [02:22:49] product atom-mapping number 2 found multiple times. -91: [02:22:49] product atom-mapping number 3 found multiple times. -91: [02:22:49] product atom-mapping number 1 found multiple times. -91: [02:22:49] product atom-mapping number 4 found multiple times. +91: [23:09:38] product atom-mapping number 5 found multiple times. +91: [23:09:38] product atom-mapping number 2 found multiple times. +91: [23:09:38] product atom-mapping number 3 found multiple times. +91: [23:09:38] product atom-mapping number 1 found multiple times. +91: [23:09:38] product atom-mapping number 4 found multiple times. +91: [23:09:38] product atom-mapping number 5 found multiple times. +91: [23:09:38] product atom-mapping number 2 found multiple times. +91: [23:09:38] product atom-mapping number 3 found multiple times. +91: [23:09:38] product atom-mapping number 1 found multiple times. +91: [23:09:38] product atom-mapping number 4 found multiple times. 91: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -91: [02:22:49] product atom-mapping number 5 found multiple times. -91: [02:22:49] product atom-mapping number 2 found multiple times. -91: [02:22:49] product atom-mapping number 3 found multiple times. -91: [02:22:49] product atom-mapping number 1 found multiple times. -91: [02:22:49] product atom-mapping number 4 found multiple times. -91: [02:22:49] product atom-mapping number 5 found multiple times. -91: [02:22:49] product atom-mapping number 2 found multiple times. -91: [02:22:49] product atom-mapping number 3 found multiple times. -91: [02:22:49] product atom-mapping number 1 found multiple times. -91: [02:22:49] product atom-mapping number 4 found multiple times. +91: [23:09:38] product atom-mapping number 5 found multiple times. +91: [23:09:38] product atom-mapping number 2 found multiple times. +91: [23:09:38] product atom-mapping number 3 found multiple times. +91: [23:09:38] product atom-mapping number 1 found multiple times. +91: [23:09:38] product atom-mapping number 4 found multiple times. +91: [23:09:38] product atom-mapping number 5 found multiple times. +91: [23:09:38] product atom-mapping number 2 found multiple times. +91: [23:09:38] product atom-mapping number 3 found multiple times. +91: [23:09:38] product atom-mapping number 1 found multiple times. +91: [23:09:38] product atom-mapping number 4 found multiple times. 91: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -91: [02:22:49] product atom-mapping number 2 found multiple times. -91: [02:22:49] product atom-mapping number 3 found multiple times. -91: [02:22:49] product atom-mapping number 1 found multiple times. -91: [02:22:49] product atom-mapping number 4 found multiple times. -91: [02:22:49] product atom-mapping number 2 found multiple times. -91: [02:22:49] product atom-mapping number 3 found multiple times. -91: [02:22:49] product atom-mapping number 1 found multiple times. -91: [02:22:49] product atom-mapping number 4 found multiple times. +91: [23:09:38] product atom-mapping number 2 found multiple times. +91: [23:09:38] product atom-mapping number 3 found multiple times. +91: [23:09:38] product atom-mapping number 1 found multiple times. +91: [23:09:38] product atom-mapping number 4 found multiple times. +91: [23:09:38] product atom-mapping number 2 found multiple times. +91: [23:09:38] product atom-mapping number 3 found multiple times. +91: [23:09:38] product atom-mapping number 1 found multiple times. +91: [23:09:38] product atom-mapping number 4 found multiple times. 91: F[C@@](Cl)(Br)O[C@](F)(Cl)Br -91: [02:22:49] product atom-mapping number 2 found multiple times. -91: [02:22:49] product atom-mapping number 3 found multiple times. -91: [02:22:49] product atom-mapping number 1 found multiple times. -91: [02:22:49] product atom-mapping number 4 found multiple times. -91: [02:22:49] product atom-mapping number 2 found multiple times. -91: [02:22:49] product atom-mapping number 3 found multiple times. -91: [02:22:49] product atom-mapping number 1 found multiple times. -91: [02:22:49] product atom-mapping number 4 found multiple times. +91: [23:09:38] product atom-mapping number 2 found multiple times. +91: [23:09:38] product atom-mapping number 3 found multiple times. +91: [23:09:38] product atom-mapping number 1 found multiple times. +91: [23:09:38] product atom-mapping number 4 found multiple times. +91: [23:09:38] product atom-mapping number 2 found multiple times. +91: [23:09:38] product atom-mapping number 3 found multiple times. +91: [23:09:38] product atom-mapping number 1 found multiple times. +91: [23:09:38] product atom-mapping number 4 found multiple times. 91: F[C@](Cl)(Br)O[C@](F)(Cl)Br -91: [02:22:49] product atom-mapping number 4 found multiple times. -91: [02:22:49] product atom-mapping number 3 found multiple times. -91: [02:22:49] product atom-mapping number 2 found multiple times. -91: [02:22:49] product atom-mapping number 1 found multiple times. -91: [02:22:49] product atom-mapping number 4 found multiple times. -91: [02:22:49] product atom-mapping number 3 found multiple times. -91: [02:22:49] product atom-mapping number 2 found multiple times. -91: [02:22:49] product atom-mapping number 1 found multiple times. -91: [02:22:49] product atom-mapping number 4 found multiple times. -91: [02:22:49] product atom-mapping number 3 found multiple times. -91: [02:22:49] product atom-mapping number 2 found multiple times. -91: [02:22:49] product atom-mapping number 1 found multiple times. -91: [02:22:49] product atom-mapping number 4 found multiple times. -91: [02:22:49] product atom-mapping number 3 found multiple times. -91: [02:22:49] product atom-mapping number 2 found multiple times. -91: [02:22:49] product atom-mapping number 1 found multiple times. -91: [02:22:49] product atom-mapping number 3 found multiple times. -91: [02:22:49] product atom-mapping number 2 found multiple times. -91: [02:22:49] product atom-mapping number 1 found multiple times. -91: [02:22:49] mapped atoms in the reactants were not mapped in the products. +91: [23:09:38] product atom-mapping number 4 found multiple times. +91: [23:09:38] product atom-mapping number 3 found multiple times. +91: [23:09:38] product atom-mapping number 2 found multiple times. +91: [23:09:38] product atom-mapping number 1 found multiple times. +91: [23:09:38] product atom-mapping number 4 found multiple times. +91: [23:09:38] product atom-mapping number 3 found multiple times. +91: [23:09:38] product atom-mapping number 2 found multiple times. +91: [23:09:38] product atom-mapping number 1 found multiple times. +91: [23:09:38] product atom-mapping number 4 found multiple times. +91: [23:09:38] product atom-mapping number 3 found multiple times. +91: [23:09:38] product atom-mapping number 2 found multiple times. +91: [23:09:38] product atom-mapping number 1 found multiple times. +91: [23:09:38] product atom-mapping number 4 found multiple times. +91: [23:09:38] product atom-mapping number 3 found multiple times. +91: [23:09:38] product atom-mapping number 2 found multiple times. +91: [23:09:38] product atom-mapping number 1 found multiple times. +91: [23:09:38] product atom-mapping number 3 found multiple times. +91: [23:09:38] product atom-mapping number 2 found multiple times. +91: [23:09:38] product atom-mapping number 1 found multiple times. +91: [23:09:38] mapped atoms in the reactants were not mapped in the products. 91: unmapped numbers are: 4 -91: [02:22:49] product atom-mapping number 3 found multiple times. -91: [02:22:49] product atom-mapping number 2 found multiple times. -91: [02:22:49] product atom-mapping number 1 found multiple times. -91: [02:22:49] mapped atoms in the reactants were not mapped in the products. +91: [23:09:38] product atom-mapping number 3 found multiple times. +91: [23:09:38] product atom-mapping number 2 found multiple times. +91: [23:09:38] product atom-mapping number 1 found multiple times. +91: [23:09:38] mapped atoms in the reactants were not mapped in the products. 91: unmapped numbers are: 4 -68: [02:22:49] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -68: [02:22:49] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -91: [02:22:49] product atom-mapping number 6 not found in reactants. -91: [02:22:49] product atom-mapping number 7 not found in reactants. -91: [02:22:49] product atom-mapping number 8 not found in reactants. -91: [02:22:49] product atom-mapping number 7 not found in reactants. -91: [02:22:49] product atom-mapping number 8 not found in reactants. -91: [02:22:49] product atom-mapping number 9 not found in reactants. -91: [02:22:49] product atom-mapping number 10 not found in reactants. -91: [02:22:49] mapped atoms in the reactants were not mapped in the products. +91: [23:09:38] product atom-mapping number 6 not found in reactants. +91: [23:09:38] product atom-mapping number 7 not found in reactants. +91: [23:09:38] product atom-mapping number 8 not found in reactants. +91: [23:09:38] product atom-mapping number 7 not found in reactants. +91: [23:09:38] product atom-mapping number 8 not found in reactants. +91: [23:09:38] product atom-mapping number 9 not found in reactants. +91: [23:09:38] product atom-mapping number 10 not found in reactants. +91: [23:09:38] mapped atoms in the reactants were not mapped in the products. 91: unmapped numbers are: 6 -91: [02:22:49] product atom-mapping number 7 not found in reactants. -91: [02:22:49] product atom-mapping number 8 not found in reactants. -91: [02:22:49] product atom-mapping number 9 not found in reactants. -91: [02:22:49] product atom-mapping number 10 not found in reactants. -91: [02:22:49] mapped atoms in the reactants were not mapped in the products. +91: [23:09:38] product atom-mapping number 7 not found in reactants. +91: [23:09:38] product atom-mapping number 8 not found in reactants. +91: [23:09:38] product atom-mapping number 9 not found in reactants. +91: [23:09:38] product atom-mapping number 10 not found in reactants. +91: [23:09:38] mapped atoms in the reactants were not mapped in the products. 91: unmapped numbers are: 6 91: smi1 [C:1][C:2][C:3]([O:4])([N:5])[Cl:6]>>[C:1][C:3]([C:2])([O:4])[N:5].[ClH:6] 91: smi2 [C:1][C:2][C:3]([O:4])([N:5])[Cl:6]>>[C:1][C:3]([C:2])([O:4])[N:5].[ClH:6] - 83/230 Test #41: resMolSupplierTest ..................... Passed 3.58 sec -test 95 - Start 95: pyChemReactions - -95: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py" -95: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap -95: Test timeout computed to be: 1500 -91: [02:22:49] mapped atoms in the reactants were not mapped in the products. +91: [23:09:38] mapped atoms in the reactants were not mapped in the products. 91: unmapped numbers are: 7 8 9 10 11 12 13 14 15 16 -91: [02:22:49] product atom-mapping number 17 not found in reactants. -91: [02:22:49] product atom-mapping number 18 not found in reactants. -91: [02:22:49] mapped atoms in the reactants were not mapped in the products. +91: [23:09:38] product atom-mapping number 17 not found in reactants. +91: [23:09:38] product atom-mapping number 18 not found in reactants. +91: [23:09:38] mapped atoms in the reactants were not mapped in the products. 91: unmapped numbers are: 12 -94: Randomness seeded to: 682250316 -94: [02:22:49] atom 0 in product 0 has multiple charge specifications. -94: [02:22:49] Found a SCD/SED line with missing/empty SDT specification at line 34 -94: [02:22:49] Found a SCD/SED line with missing/empty SDT specification at line 36 -94: [02:22:49] Found a SCD/SED line with missing/empty SDT specification at line 38 -94: [02:22:49] Found a SCD/SED line with missing/empty SDT specification at line 40 -94: [02:22:49] Found a SCD/SED line with missing/empty SDT specification at line 42 -94: [02:22:49] Found a SCD/SED line with missing/empty SDT specification at line 87 -94: [02:22:49] Found a SCD/SED line with missing/empty SDT specification at line 89 -94: [02:22:49] Found a SCD/SED line with missing/empty SDT specification at line 91 -94: [02:22:49] Found a SCD/SED line with missing/empty SDT specification at line 93 -94: [02:22:49] Found a SCD/SED line with missing/empty SDT specification at line 95 -94: [02:22:49] mapped atoms in the reactants were not mapped in the products. -94: unmapped numbers are: 2 -94: [02:22:49] mapped atoms in the reactants were not mapped in the products. -94: unmapped numbers are: 2 -94: [02:22:49] SMARTS Parse Error: unclosed ring for input: 'CC1' -94: [02:22:49] SMILES Parse Error: unclosed ring for input: 'CC1' -94: [02:22:49] mapped atoms in the reactants were not mapped in the products. -94: unmapped numbers are: 2 -94: [02:22:49] product atom-mapping number 2 not found in reactants. -94: [02:22:49] mapped atoms in the reactants were not mapped in the products. -94: unmapped numbers are: 2 -94: [02:22:49] product atom-mapping number 2 not found in reactants. -94: [02:22:49] CX Extensions: Substance group hierarchy is not always preserved. -94: [02:22:49] CX Extensions: Substance group hierarchy is not always preserved. -91: [02:22:49] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) -91: [02:22:49] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +91: [23:09:38] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +91: [23:09:38] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) 91: -94: [02:22:49] reactant 0 has no mapped atoms. -94: [02:22:49] product 0 has no mapped atoms. -94: [02:22:49] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -94: [02:22:49] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -94: [02:22:49] Explicit valence for atom # 1 O, 5, is greater than permitted -94: =============================================================================== -94: All tests passed (702 assertions in 28 test cases) -94: -93: 30000000 30000000 -68: ---------------------------------- -68: ---------------------------------- -91: [02:22:49] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels +91: [23:09:38] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels 91: ------------- 91: CCOc1ccccc1 - 84/230 Test #94: rxnTestCatch ........................... Passed 0.12 sec -test 96 - Start 96: pyChemReactionEnumerations +87: [23:09:38] Explicit valence for atom # 2 O, 4, is greater than permitted +68: [23:09:38] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +68: [23:09:38] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +87: [23:09:38] Explicit valence for atom # 3 Al, 6, is greater than permitted +87: [23:09:38] Explicit valence for atom # 3 Be, 4, is greater than permitted +87: [23:09:38] Explicit valence for atom # 27 P, 6, is greater than permitted +90: Randomness seeded to: 1228956728 +90: =============================================================================== +90: All tests passed (11480 assertions in 38 test cases) +90: + 80/230 Test #90: testGenericGroups ...................... Passed 1.00 sec +test 92 + Start 92: testReactionFingerprints -96: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py" -96: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap -96: Test timeout computed to be: 1500 -68: [02:22:49] +92: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/testReactionFingerprints +92: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions +92: Test timeout computed to be: 1500 +91: [23:09:38] reactant 0 has no mapped atoms. +91: [23:09:38] product 0 has no mapped atoms. +91: [23:09:38] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. + 81/230 Test #91: testReaction ........................... Passed 0.52 sec +test 93 + Start 93: testEnumeration + +93: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/testEnumeration +93: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions +93: Test timeout computed to be: 1500 +68: ---------------------------------- +68: ---------------------------------- +68: [23:09:39] 68: 68: **** 68: Pre-condition Violation @@ -23558,44 +23500,397 @@ 68: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 68: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 68: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -68: 3# 0x0000AAAAC6F3EC20 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: 4# 0x0000AAAAC6FA44C4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: 5# 0x0000AAAAC6F155EC in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -68: 6# 0x0000FFFF7FC8229C in /lib/aarch64-linux-gnu/libc.so.6 +68: 3# 0x0000AAAACAE0EC20 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 4# 0x0000AAAACAE744C4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 5# 0x0000AAAACADE55EC in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 6# 0x0000FFFF9509229C in /lib/aarch64-linux-gnu/libc.so.6 68: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -68: 8# 0x0000AAAAC6F157B0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +68: 8# 0x0000AAAACADE57B0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 68: ---------- 68: **** 68: -68: [02:22:49] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -91: [02:22:49] reactant 0 has no mapped atoms. -91: [02:22:49] product 0 has no mapped atoms. -91: [02:22:49] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. - 85/230 Test #91: testReaction ........................... Passed 0.35 sec +68: [23:09:39] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +92: [23:09:39] ------------------------------------- +92: [23:09:39] Test Reaction StructuralFingerprint +92: [23:09:39] DEPRECATION WARNING: please use AtomPairGenerator +92: [23:09:39] DEPRECATION WARNING: please use AtomPairGenerator +92: [23:09:39] DEPRECATION WARNING: please use AtomPairGenerator +92: [23:09:39] DEPRECATION WARNING: please use AtomPairGenerator +92: [23:09:39] DEPRECATION WARNING: please use AtomPairGenerator +92: [23:09:39] DEPRECATION WARNING: please use AtomPairGenerator +92: [23:09:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +92: [23:09:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +92: [23:09:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +92: [23:09:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +92: [23:09:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +92: [23:09:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +92: [23:09:39] ------------------------------------- +92: [23:09:39] Test Reaction DifferenceFingerprint +92: [23:09:39] DEPRECATION WARNING: please use AtomPairGenerator +92: [23:09:39] DEPRECATION WARNING: please use AtomPairGenerator +92: [23:09:39] DEPRECATION WARNING: please use AtomPairGenerator +92: [23:09:39] DEPRECATION WARNING: please use AtomPairGenerator +92: [23:09:39] DEPRECATION WARNING: please use AtomPairGenerator +92: [23:09:39] DEPRECATION WARNING: please use AtomPairGenerator +92: [23:09:39] DEPRECATION WARNING: please use AtomPairGenerator +92: [23:09:39] DEPRECATION WARNING: please use AtomPairGenerator +92: [23:09:39] DEPRECATION WARNING: please use AtomPairGenerator +92: [23:09:39] DEPRECATION WARNING: please use AtomPairGenerator +92: [23:09:39] DEPRECATION WARNING: please use AtomPairGenerator +92: [23:09:39] DEPRECATION WARNING: please use AtomPairGenerator +92: [23:09:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +92: [23:09:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +92: [23:09:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +92: [23:09:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator + 82/230 Test #92: testReactionFingerprints ............... Passed 0.12 sec +test 94 + Start 94: rxnTestCatch + +94: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/rxnTestCatch +94: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions +94: Test timeout computed to be: 1500 +94: Randomness seeded to: 832497901 +94: [23:09:39] atom 0 in product 0 has multiple charge specifications. +94: [23:09:39] Found a SCD/SED line with missing/empty SDT specification at line 34 +94: [23:09:39] Found a SCD/SED line with missing/empty SDT specification at line 36 +94: [23:09:39] Found a SCD/SED line with missing/empty SDT specification at line 38 +94: [23:09:39] Found a SCD/SED line with missing/empty SDT specification at line 40 +94: [23:09:39] Found a SCD/SED line with missing/empty SDT specification at line 42 +94: [23:09:39] Found a SCD/SED line with missing/empty SDT specification at line 87 +94: [23:09:39] Found a SCD/SED line with missing/empty SDT specification at line 89 +94: [23:09:39] Found a SCD/SED line with missing/empty SDT specification at line 91 +94: [23:09:39] Found a SCD/SED line with missing/empty SDT specification at line 93 +94: [23:09:39] Found a SCD/SED line with missing/empty SDT specification at line 95 +94: [23:09:39] mapped atoms in the reactants were not mapped in the products. +94: unmapped numbers are: 2 +94: [23:09:39] mapped atoms in the reactants were not mapped in the products. +94: unmapped numbers are: 2 +94: [23:09:39] SMARTS Parse Error: unclosed ring for input: 'CC1' +94: [23:09:39] SMILES Parse Error: unclosed ring for input: 'CC1' +94: [23:09:39] mapped atoms in the reactants were not mapped in the products. +94: unmapped numbers are: 2 +94: [23:09:39] product atom-mapping number 2 not found in reactants. +94: [23:09:39] mapped atoms in the reactants were not mapped in the products. +94: unmapped numbers are: 2 +94: [23:09:39] product atom-mapping number 2 not found in reactants. +94: [23:09:39] CX Extensions: Substance group hierarchy is not always preserved. +94: [23:09:39] CX Extensions: Substance group hierarchy is not always preserved. +94: [23:09:39] reactant 0 has no mapped atoms. +94: [23:09:39] product 0 has no mapped atoms. +94: [23:09:39] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +94: [23:09:39] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +94: [23:09:39] Explicit valence for atom # 1 O, 5, is greater than permitted +94: =============================================================================== +94: All tests passed (702 assertions in 28 test cases) +94: + 83/230 Test #94: rxnTestCatch ........................... Passed 0.29 sec +test 95 + Start 95: pyChemReactions + +95: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py" +95: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap +95: Test timeout computed to be: 1500 +93: 30000000 30000000 +68: [23:09:39] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +68: [23:09:39] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' +87: [23:09:39] Explicit valence for atom # 9 N, 6, is greater than permitted +68: [23:09:39] Empty atom list: 'M ALS 1 0 F' on line 8. + 84/230 Test #68: fileParsersTest1 ....................... Passed 6.65 sec +test 96 + Start 96: pyChemReactionEnumerations + +96: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py" +96: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap +96: Test timeout computed to be: 1500 + 85/230 Test #41: resMolSupplierTest ..................... Passed 9.40 sec test 97 Start 97: pyChemReactionSanitize 97: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/testSanitize.py" 97: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap 97: Test timeout computed to be: 1500 -87: Randomness seeded to: 1100420496 -87: [02:22:49] Explicit valence for atom # 9 N, 6, is greater than permitted -87: [02:22:49] Explicit valence for atom # 3 Al, 6, is greater than permitted -87: [02:22:49] Explicit valence for atom # 4 Al, 6, is greater than permitted -87: [02:22:49] Explicit valence for atom # 10 Si, 6, is greater than permitted -68: [02:22:49] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -68: [02:22:49] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -68: [02:22:50] Empty atom list: 'M ALS 1 0 F' on line 8. - 86/230 Test #68: fileParsersTest1 ....................... Passed 3.03 sec +87: [23:09:40] Explicit valence for atom # 3 Al, 6, is greater than permitted +95: ...[23:09:40] +95: +95: **** +95: Pre-condition Violation +95: getNumImplicitHs() called without preceding call to calcImplicitValence() +95: Violation occurred on line 302 in file ./Code/GraphMol/Atom.cpp +95: Failed Expression: d_implicitValence > -1 +95: ---------- +95: Stacktrace: +95: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +95: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +95: 2# RDKit::Atom::getNumImplicitHs() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +95: 3# RDKit::Atom::getTotalNumHs(bool) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +95: 4# Queries::EqualityQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 +95: 5# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +95: 6# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +95: 7# Queries::OrQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +95: 8# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +95: 9# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +95: 10# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +95: 11# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +95: 12# RDKit::detail::RecursiveMatcher(RDKit::ROMol const&, RDKit::ROMol const&, std::vector >&, std::map*, std::less, std::allocator*> > >&, RDKit::SubstructMatchParameters const&, std::vector >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +95: 13# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +95: 14# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +95: 15# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +95: 16# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +95: 17# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +95: 18# RDKit::ReactionRunnerUtils::getReactantMatchesToTemplate(RDKit::ROMol const&, RDKit::ROMol const&, unsigned int, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 +95: 19# RDKit::ReactionRunnerUtils::getReactantMatches(std::vector, std::allocator > > const&, RDKit::ChemicalReaction const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >, std::allocator, std::allocator > >, std::allocator, std::allocator > > > > > >&, unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 +95: 20# RDKit::run_Reactants(RDKit::ChemicalReaction const&, std::vector, std::allocator > > const&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 +95: 21# RDKit::ChemicalReaction::runReactants(std::vector, std::allocator > >, unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 +95: 22# _object* RDKit::RunReactants(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +95: 23# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +95: 24# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +95: 25# 0x0000FFFFB9ED15C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +95: 26# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +95: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so +95: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so +95: 29# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +95: 30# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +95: 31# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so +95: 32# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +95: 33# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +95: 34# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +95: 35# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +95: 36# 0x0000FFFFB79B4180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +95: 37# 0x0000FFFFB79B4118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +95: 38# 0x0000FFFFB79B40A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +95: 39# 0x0000FFFFB79B4040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +95: 40# 0x0000FFFFB79B3FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +95: 41# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so +95: 42# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so +95: 43# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so +95: 44# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so +95: 45# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +95: 46# 0x0000FFFFB9ECE19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +95: 47# _PyObject_MakeTpCall in /usr/bin/python3 +95: 48# _PyEval_EvalFrameDefault in /usr/bin/python3 +95: 49# 0x00000000004C3D1C in /usr/bin/python3 +95: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 +95: 51# _PyObject_Call_Prepend in /usr/bin/python3 +95: 52# 0x000000000052608C in /usr/bin/python3 +95: 53# _PyObject_MakeTpCall in /usr/bin/python3 +95: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 +95: 55# 0x00000000004C3D1C in /usr/bin/python3 +95: 56# _PyEval_EvalFrameDefault in /usr/bin/python3 +95: 57# _PyObject_Call_Prepend in /usr/bin/python3 +95: 58# 0x000000000052608C in /usr/bin/python3 +95: 59# _PyObject_MakeTpCall in /usr/bin/python3 +95: 60# _PyEval_EvalFrameDefault in /usr/bin/python3 +95: 61# 0x00000000004C3D1C in /usr/bin/python3 +95: 62# _PyEval_EvalFrameDefault in /usr/bin/python3 +95: 63# _PyObject_Call_Prepend in /usr/bin/python3 +95: 64# 0x000000000052608C in /usr/bin/python3 +95: 65# _PyObject_MakeTpCall in /usr/bin/python3 +95: 66# _PyEval_EvalFrameDefault in /usr/bin/python3 +95: 67# _PyObject_Call_Prepend in /usr/bin/python3 +95: 68# 0x000000000051FB4C in /usr/bin/python3 +95: 69# 0x000000000051B324 in /usr/bin/python3 +95: 70# _PyObject_MakeTpCall in /usr/bin/python3 +95: 71# _PyEval_EvalFrameDefault in /usr/bin/python3 +95: 72# PyEval_EvalCode in /usr/bin/python3 +95: 73# 0x0000000000595200 in /usr/bin/python3 +95: 74# 0x00000000006757AC in /usr/bin/python3 +95: 75# _PyRun_SimpleFileObject in /usr/bin/python3 +95: 76# _PyRun_AnyFileObject in /usr/bin/python3 +95: 77# Py_RunMain in /usr/bin/python3 +95: 78# Py_BytesMain in /usr/bin/python3 +95: 79# 0x0000FFFFBA8D229C in /lib/aarch64-linux-gnu/libc.so.6 +95: 80# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +95: 81# _start in /usr/bin/python3 +95: ---------- +95: **** +95: +95: [23:09:40] +95: +95: **** +95: Pre-condition Violation +95: getNumImplicitHs() called without preceding call to calcImplicitValence() +95: Violation occurred on line 302 in file ./Code/GraphMol/Atom.cpp +95: Failed Expression: d_implicitValence > -1 +95: ---------- +95: Stacktrace: +95: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +95: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +95: 2# RDKit::Atom::getNumImplicitHs() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +95: 3# RDKit::Atom::getTotalNumHs(bool) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +95: 4# Queries::EqualityQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 +95: 5# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +95: 6# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +95: 7# Queries::OrQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +95: 8# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +95: 9# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +95: 10# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +95: 11# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +95: 12# RDKit::detail::RecursiveMatcher(RDKit::ROMol const&, RDKit::ROMol const&, std::vector >&, std::map*, std::less, std::allocator*> > >&, RDKit::SubstructMatchParameters const&, std::vector >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +95: 13# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +95: 14# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +95: 15# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +95: 16# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +95: 17# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +95: 18# RDKit::ReactionRunnerUtils::getReactantMatchesToTemplate(RDKit::ROMol const&, RDKit::ROMol const&, unsigned int, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 +95: 19# RDKit::ReactionRunnerUtils::getReactantMatches(std::vector, std::allocator > > const&, RDKit::ChemicalReaction const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >, std::allocator, std::allocator > >, std::allocator, std::allocator > > > > > >&, unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 +95: 20# RDKit::run_Reactants(RDKit::ChemicalReaction const&, std::vector, std::allocator > > const&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 +95: 21# RDKit::ChemicalReaction::runReactants(std::vector, std::allocator > >, unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 +95: 22# _object* RDKit::RunReactants(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +95: 23# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +95: 24# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +95: 25# 0x0000FFFFB9ED15C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +95: 26# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +95: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so +95: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so +95: 29# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +95: 30# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +95: 31# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so +95: 32# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +95: 33# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +95: 34# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +95: 35# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +95: 36# 0x0000FFFFB79B4180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +95: 37# 0x0000FFFFB79B4118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +95: 38# 0x0000FFFFB79B40A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +95: 39# 0x0000FFFFB79B4040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +95: 40# 0x0000FFFFB79B3FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +95: 41# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so +95: 42# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so +95: 43# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so +95: 44# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so +95: 45# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +95: 46# 0x0000FFFFB9ECE19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +95: 47# _PyObject_MakeTpCall in /usr/bin/python3 +95: 48# _PyEval_EvalFrameDefault in /usr/bin/python3 +95: 49# 0x00000000004C3D1C in /usr/bin/python3 +95: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 +95: 51# _PyObject_Call_Prepend in /usr/bin/python3 +95: 52# 0x000000000052608C in /usr/bin/python3 +95: 53# _PyObject_MakeTpCall in /usr/bin/python3 +95: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 +95: 55# 0x00000000004C3D1C in /usr/bin/python3 +95: 56# _PyEval_EvalFrameDefault in /usr/bin/python3 +95: 57# _PyObject_Call_Prepend in /usr/bin/python3 +95: 58# 0x000000000052608C in /usr/bin/python3 +95: 59# _PyObject_MakeTpCall in /usr/bin/python3 +95: 60# _PyEval_EvalFrameDefault in /usr/bin/python3 +95: 61# 0x00000000004C3D1C in /usr/bin/python3 +95: 62# _PyEval_EvalFrameDefault in /usr/bin/python3 +95: 63# _PyObject_Call_Prepend in /usr/bin/python3 +95: 64# 0x000000000052608C in /usr/bin/python3 +95: 65# _PyObject_MakeTpCall in /usr/bin/python3 +95: 66# _PyEval_EvalFrameDefault in /usr/bin/python3 +95: 67# _PyObject_Call_Prepend in /usr/bin/python3 +95: 68# 0x000000000051FB4C in /usr/bin/python3 +95: 69# 0x000000000051B324 in /usr/bin/python3 +95: 70# _PyObject_MakeTpCall in /usr/bin/python3 +95: 71# _PyEval_EvalFrameDefault in /usr/bin/python3 +95: 72# PyEval_EvalCode in /usr/bin/python3 +95: 73# 0x0000000000595200 in /usr/bin/python3 +95: 74# 0x00000000006757AC in /usr/bin/python3 +95: 75# _PyRun_SimpleFileObject in /usr/bin/python3 +95: 76# _PyRun_AnyFileObject in /usr/bin/python3 +95: 77# Py_RunMain in /usr/bin/python3 +95: 78# Py_BytesMain in /usr/bin/python3 +95: 79# 0x0000FFFFBA8D229C in /lib/aarch64-linux-gnu/libc.so.6 +95: 80# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +95: 81# _start in /usr/bin/python3 +95: ---------- +95: **** +95: +95: .........[23:09:40] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +95: [23:09:40] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +95: [23:09:40] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +95: [23:09:40] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +95: .[23:09:40] product atom-mapping number 1 found multiple times. +95: [23:09:40] product atom-mapping number 1 found multiple times. +95: ................[23:09:40] mapped atoms in the reactants were not mapped in the products. +95: unmapped numbers are: 3 +95: [23:09:40] mapped atoms in the reactants were not mapped in the products. +95: unmapped numbers are: 3 +95: .[23:09:40] mapped atoms in the reactants were not mapped in the products. +95: unmapped numbers are: 3 +95: ..[23:09:40] reactant 2 has no mapped atoms. +95: [23:09:40] reactant 2 has no mapped atoms. +95: [23:09:40] product 1 has no mapped atoms. +96: [23:09:40] == testCartesianProduct +95: ........[23:09:40] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q +95: [23:09:40] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' +95: [23:09:40] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q +95: [23:09:40] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' +95: .[23:09:40] reactant atom-mapping number 1 found multiple times. +95: [23:09:40] product atom-mapping number 2 not found in reactants. +95: [23:09:40] mapped atoms in the reactants were not mapped in the products. +95: unmapped numbers are: 4 +95: [23:09:40] product atom-mapping number 5 not found in reactants. +96: .[23:09:40] == testEnumerateLibrary +96: /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py:266: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/testData/enumeration.pickle'> +96: open(os.path.join(self.dataDir, "enumeration.pickle"), 'rb').read()) +96: ResourceWarning: Enable tracemalloc to get the object allocation traceback +95: ........./build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:745: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/testData/reaction1.no_metadata.png'> +95: png = open(fname, 'rb').read() +95: ResourceWarning: Enable tracemalloc to get the object allocation traceback +95: [23:09:40] Found a SCD/SED line with missing/empty SDT specification at line 34 +95: [23:09:40] Found a SCD/SED line with missing/empty SDT specification at line 36 +95: [23:09:40] Found a SCD/SED line with missing/empty SDT specification at line 38 +95: [23:09:40] Found a SCD/SED line with missing/empty SDT specification at line 40 +95: [23:09:40] Found a SCD/SED line with missing/empty SDT specification at line 42 +95: [23:09:40] Found a SCD/SED line with missing/empty SDT specification at line 87 +95: [23:09:40] Found a SCD/SED line with missing/empty SDT specification at line 89 +95: [23:09:40] Found a SCD/SED line with missing/empty SDT specification at line 91 +95: [23:09:40] Found a SCD/SED line with missing/empty SDT specification at line 93 +95: [23:09:40] Found a SCD/SED line with missing/empty SDT specification at line 95 +87: [23:09:40] Explicit valence for atom # 4 Al, 6, is greater than permitted +96: ..[23:09:40] == testRGroupState +96: .[23:09:40] == testRandomEnumerateAllBBsLibrary +96: ** [1, 1] +96: ** [0, 2] +96: ** [1, 0] +96: .[23:09:40] == testRandomEnumerateLibrary +96: .[23:09:40] == testRandomSample +96: .[23:09:40] == testRandomSampleAllBBs +96: .[23:09:40] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +96: [23:09:40] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +96: .[23:09:40] == testRemoveBadMatches +95: ..[23:09:40] SMARTS Parse Error: syntax error while parsing: boromicacid +95: [23:09:41] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +95: [23:09:41] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +95: [23:09:41] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +95: [23:09:41] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +95: [23:09:41] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +95: [23:09:41] reaction has no reactants +95: [23:09:41] reaction has no products +95: [23:09:41] initialization failed +95: [23:09:41] reaction has no reactants +95: [23:09:41] reaction has no products +96: .[23:09:41] == testTimings +87: [23:09:41] Explicit valence for atom # 10 Si, 6, is greater than permitted +95: .[23:09:41] SMARTS Parse Error: syntax error while parsing: boromicacid +95: [23:09:41] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +95: [23:09:41] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +95: [23:09:41] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +95: [23:09:41] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +95: [23:09:41] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +95: [23:09:41] reaction has no reactants +95: [23:09:41] reaction has no products +95: [23:09:41] initialization failed +95: [23:09:41] reaction has no reactants +95: [23:09:41] reaction has no products +95: . +95: ---------------------------------------------------------------------- +95: Ran 54 tests in 0.492s +95: +95: OK +95: ******************************************** +95: /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/testData/AmideBond.rxn +95: + 86/230 Test #95: pyChemReactions ........................ Passed 1.93 sec test 98 Start 98: testChemTransforms 98: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/testChemTransforms 98: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms 98: Test timeout computed to be: 1500 -87: [02:22:50] Explicit valence for atom # 2 O, 4, is greater than permitted -87: [02:22:50] Explicit valence for atom # 3 Al, 6, is greater than permitted -87: [02:22:50] Explicit valence for atom # 3 Be, 4, is greater than permitted 98: 1 smi: CC 98: 1 smi: CC 98: 2 smi: CCO[C@H](N)P @@ -23604,240 +23899,54 @@ 98: replaceSub smi1:CCNCC 98: sidechains chiral=true smi1;;; [1*]P([2*])[C@H](N)O 98: sidechains chiral=false smi1;;; [1*]P([2*])[C@H](N)O -87: [02:22:50] Explicit valence for atom # 27 P, 6, is greater than permitted -98: [02:22:50] SMARTS Parse Error: syntax error while parsing: bar -98: [02:22:50] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' - 87/230 Test #98: testChemTransforms ..................... Passed 0.08 sec -test 99 - Start 99: chemTransformsTestCatch - -99: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms -99: Test timeout computed to be: 1500 -99: Randomness seeded to: 2982037809 -99: [02:22:50] Incomplete atom labelling, cannot make bond -99: [02:22:50] -99: -99: **** -99: Invariant Violation -99: molzip: bond info already exists for end atom with label:1 -99: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -99: Failed Expression: !bond.b -99: ---------- -99: Stacktrace: -99: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -99: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -99: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -99: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -99: 4# 0x0000AAAAEA9D69A0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 5# 0x0000AAAAEAA25A4C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 6# 0x0000AAAAEAA26400 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 7# 0x0000AAAAEAA26834 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 8# 0x0000AAAAEA9FAEF8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 9# 0x0000AAAAEA9FB444 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 10# 0x0000AAAAEA9CBE90 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 11# 0x0000FFFF95CF229C in /lib/aarch64-linux-gnu/libc.so.6 -99: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -99: 13# 0x0000AAAAEA9CBF70 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: ---------- -99: **** -99: -99: [02:22:50] Incomplete atom labelling, cannot make bond -99: [02:22:50] -99: -99: **** -99: Invariant Violation -99: molzip: bond info already exists for end atom with label:1 -99: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -99: Failed Expression: !bond.b -99: ---------- -99: Stacktrace: -99: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -99: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -99: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -99: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -99: 4# 0x0000AAAAEA9D69A0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 5# 0x0000AAAAEAA25A4C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 6# 0x0000AAAAEAA26400 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 7# 0x0000AAAAEAA26834 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 8# 0x0000AAAAEA9FAEF8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 9# 0x0000AAAAEA9FB444 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 10# 0x0000AAAAEA9CBE90 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 11# 0x0000FFFF95CF229C in /lib/aarch64-linux-gnu/libc.so.6 -99: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -99: 13# 0x0000AAAAEA9CBF70 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: ---------- -99: **** -99: -99: [02:22:50] Incomplete atom labelling, cannot make bond -99: [02:22:50] -99: -99: **** -99: Invariant Violation -99: molzip: bond info already exists for end atom with label:1 -99: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -99: Failed Expression: !bond.b -99: ---------- -99: Stacktrace: -99: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -99: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -99: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -99: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -99: 4# 0x0000AAAAEA9D69A0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 5# 0x0000AAAAEAA25A4C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 6# 0x0000AAAAEAA26400 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 7# 0x0000AAAAEAA26834 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 8# 0x0000AAAAEA9FAEF8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 9# 0x0000AAAAEA9FB444 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 10# 0x0000AAAAEA9CBE90 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 11# 0x0000FFFF95CF229C in /lib/aarch64-linux-gnu/libc.so.6 -99: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -99: 13# 0x0000AAAAEA9CBF70 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: ---------- -99: **** -99: -99: [02:22:50] Incomplete atom labelling, cannot make bond -99: [02:22:50] Incomplete atom labelling, cannot make bond -99: [02:22:50] Incomplete atom labelling, cannot make bond -99: [02:22:50] -99: -99: **** -99: Invariant Violation -99: molzip: bond info already exists for end atom with label:1 -99: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -99: Failed Expression: !bond.b -99: ---------- -99: Stacktrace: -99: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -99: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -99: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -99: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -99: 4# 0x0000AAAAEA9D69A0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 5# 0x0000AAAAEAA25A4C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 6# 0x0000AAAAEAA26400 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 7# 0x0000AAAAEAA26834 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 8# 0x0000AAAAEA9FAEF8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 9# 0x0000AAAAEA9FB444 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 10# 0x0000AAAAEA9CBE90 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 11# 0x0000FFFF95CF229C in /lib/aarch64-linux-gnu/libc.so.6 -99: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -99: 13# 0x0000AAAAEA9CBF70 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: ---------- -99: **** -99: -99: [02:22:50] Incomplete atom labelling, cannot make bond -99: [02:22:50] -99: -99: **** -99: Invariant Violation -99: molzip: bond info already exists for end atom with label:1 -99: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -99: Failed Expression: !bond.b -99: ---------- -99: Stacktrace: -99: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -99: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -99: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -99: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -99: 4# 0x0000AAAAEA9D69A0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 5# 0x0000AAAAEAA25A4C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 6# 0x0000AAAAEAA26400 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 7# 0x0000AAAAEAA26834 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 8# 0x0000AAAAEA9FAEF8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 9# 0x0000AAAAEA9FB444 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 10# 0x0000AAAAEA9CBE90 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 11# 0x0000FFFF95CF229C in /lib/aarch64-linux-gnu/libc.so.6 -99: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -99: 13# 0x0000AAAAEA9CBF70 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: ---------- -99: **** -99: -99: [02:22:50] -99: -99: **** -99: Invariant Violation -99: molzip: zipped Bond already exists, perhaps labels are duplicated -99: Violation occurred on line 742 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -99: Failed Expression: params.label == MolzipLabel::FragmentOnBonds || !a->getOwningMol().getBondBetweenAtoms(a->getIdx(), b->getIdx()) -99: ---------- -99: Stacktrace: -99: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -99: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -99: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -99: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -99: 4# RDKit::molzip(RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -99: 5# 0x0000AAAAEA9CCC58 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 6# 0x0000AAAAEAA25A4C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 7# 0x0000AAAAEAA26400 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 8# 0x0000AAAAEAA26834 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 9# 0x0000AAAAEA9FAEF8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 10# 0x0000AAAAEA9FB444 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 11# 0x0000AAAAEA9CBE90 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: 12# 0x0000FFFF95CF229C in /lib/aarch64-linux-gnu/libc.so.6 -99: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -99: 14# 0x0000AAAAEA9CBF70 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -99: ---------- -99: **** -99: -99: =============================================================================== -99: All tests passed (674 assertions in 9 test cases) -99: - 88/230 Test #99: chemTransformsTestCatch ................ Passed 0.06 sec -test 100 - Start 100: tautomerQueryTestCatch - -100: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch -100: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery -100: Test timeout computed to be: 1500 -97: .[02:22:50] reactant 0 has no mapped atoms. -97: [02:22:50] product 0 has no mapped atoms. -97: [02:22:50] reactant 0 has no mapped atoms. -97: [02:22:50] product 0 has no mapped atoms. -95: ...[02:22:50] -95: -95: **** -97: .[02:22:50] reactant 0 has no mapped atoms. -97: [02:22:50] reactant 1 has no mapped atoms. -97: [02:22:50] product 0 has no mapped atoms. -97: [02:22:50] reactant 0 has no mapped atoms. -97: [02:22:50] reactant 1 has no mapped atoms. -97: [02:22:50] product 0 has no mapped atoms. -97: [02:22:50] reactant 0 has no mapped atoms. -97: [02:22:50] reactant 1 has no mapped atoms. -97: [02:22:50] product 0 has no mapped atoms. -97: [02:22:50] reactant 0 has no mapped atoms. -97: [02:22:50] reactant 1 has no mapped atoms. -97: [02:22:50] product 0 has no mapped atoms. -97: [02:22:50] reactant 0 has no mapped atoms. -97: [02:22:50] reactant 1 has no mapped atoms. -97: [02:22:50] product 0 has no mapped atoms. -97: [02:22:50] reactant 0 has no mapped atoms. -97: [02:22:50] reactant 1 has no mapped atoms. -97: [02:22:50] product 0 has no mapped atoms. -97: [02:22:50] reactant 0 has no mapped atoms. -97: [02:22:50] reactant 1 has no mapped atoms. -97: [02:22:50] product 0 has no mapped atoms. -97: [02:22:50] reactant 0 has no mapped atoms. -97: [02:22:50] reactant 1 has no mapped atoms. -97: [02:22:50] product 0 has no mapped atoms. -97: [02:22:50] reactant 0 has no mapped atoms. -97: [02:22:50] reactant 1 has no mapped atoms. -97: [02:22:50] product 0 has no mapped atoms. -97: [02:22:50] reactant 0 has no mapped atoms. -97: [02:22:50] reactant 1 has no mapped atoms. -97: [02:22:50] product 0 has no mapped atoms. -97: [02:22:50] reactant 0 has no mapped atoms. -97: [02:22:50] reactant 1 has no mapped atoms. -97: [02:22:50] product 0 has no mapped atoms. -97: [02:22:50] reactant 0 has no mapped atoms. -97: [02:22:50] reactant 1 has no mapped atoms. -97: [02:22:50] product 0 has no mapped atoms. -97: [02:22:50] reactant 0 has no mapped atoms. -97: [02:22:50] reactant 1 has no mapped atoms. -97: [02:22:50] product 0 has no mapped atoms. -97: [02:22:50] reactant 0 has no mapped atoms. -97: [02:22:50] reactant 1 has no mapped atoms. -97: [02:22:50] product 0 has no mapped atoms. +98: [23:09:41] SMARTS Parse Error: syntax error while parsing: bar +98: [23:09:41] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' +97: .[23:09:41] reactant 0 has no mapped atoms. +97: [23:09:41] product 0 has no mapped atoms. +97: [23:09:41] reactant 0 has no mapped atoms. +97: [23:09:41] product 0 has no mapped atoms. +97: .[23:09:41] reactant 0 has no mapped atoms. +97: [23:09:41] reactant 1 has no mapped atoms. +97: [23:09:41] product 0 has no mapped atoms. +97: [23:09:41] reactant 0 has no mapped atoms. +97: [23:09:41] reactant 1 has no mapped atoms. +97: [23:09:41] product 0 has no mapped atoms. +97: [23:09:41] reactant 0 has no mapped atoms. +97: [23:09:41] reactant 1 has no mapped atoms. +97: [23:09:41] product 0 has no mapped atoms. +97: [23:09:41] reactant 0 has no mapped atoms. +97: [23:09:41] reactant 1 has no mapped atoms. +97: [23:09:41] product 0 has no mapped atoms. +97: [23:09:41] reactant 0 has no mapped atoms. +97: [23:09:41] reactant 1 has no mapped atoms. +97: [23:09:41] product 0 has no mapped atoms. +97: [23:09:41] reactant 0 has no mapped atoms. +97: [23:09:41] reactant 1 has no mapped atoms. +97: [23:09:41] product 0 has no mapped atoms. +97: [23:09:41] reactant 0 has no mapped atoms. +97: [23:09:41] reactant 1 has no mapped atoms. +97: [23:09:41] product 0 has no mapped atoms. +97: [23:09:41] reactant 0 has no mapped atoms. +97: [23:09:41] reactant 1 has no mapped atoms. +97: [23:09:41] product 0 has no mapped atoms. +97: [23:09:41] reactant 0 has no mapped atoms. +97: [23:09:41] reactant 1 has no mapped atoms. +97: [23:09:41] product 0 has no mapped atoms. +97: [23:09:41] reactant 0 has no mapped atoms. +97: [23:09:41] reactant 1 has no mapped atoms. +97: [23:09:41] product 0 has no mapped atoms. +97: [23:09:41] reactant 0 has no mapped atoms. +97: [23:09:41] reactant 1 has no mapped atoms. +97: [23:09:41] product 0 has no mapped atoms. +97: [23:09:41] reactant 0 has no mapped atoms. +97: [23:09:41] reactant 1 has no mapped atoms. +97: [23:09:41] product 0 has no mapped atoms. +97: [23:09:41] reactant 0 has no mapped atoms. +97: [23:09:41] reactant 1 has no mapped atoms. +97: [23:09:41] product 0 has no mapped atoms. +97: [23:09:41] reactant 0 has no mapped atoms. +97: [23:09:41] reactant 1 has no mapped atoms. +97: [23:09:41] product 0 has no mapped atoms. 97: () 97: ******************************************** 97: $RXN @@ -24201,110 +24310,16 @@ 97: 1 2 1 0 97: M ISO 2 1 1 2 2 97: M END -97: [02:22:50] reactant 0 has no mapped atoms. -97: [02:22:50] reactant 1 has no mapped atoms. -97: [02:22:50] product 0 has no mapped atoms. -97: [02:22:50] Could not find RLabel mapping for atom: 0 in template: 1 -97: [02:22:50] reactant 1 has no mapped atoms. -97: [02:22:50] reactant 1 has no mapped atoms. -97: [02:22:50] reactant 1 has no mapped atoms. -95: Pre-condition Violation -95: getNumImplicitHs() called without preceding call to calcImplicitValence() -95: Violation occurred on line 302 in file ./Code/GraphMol/Atom.cpp -95: Failed Expression: d_implicitValence > -1 -95: ---------- -95: Stacktrace: -95: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -95: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -95: 2# RDKit::Atom::getNumImplicitHs() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -95: 3# RDKit::Atom::getTotalNumHs(bool) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -95: 4# Queries::EqualityQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 -95: 5# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -95: 6# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -95: 7# Queries::OrQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -95: 8# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -95: 9# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -95: 10# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -95: 11# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -95: 12# RDKit::detail::RecursiveMatcher(RDKit::ROMol const&, RDKit::ROMol const&, std::vector >&, std::map*, std::less, std::allocator*> > >&, RDKit::SubstructMatchParameters const&, std::vector >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -95: 13# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -95: 14# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -95: 15# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -95: 16# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -95: 17# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -95: 18# RDKit::ReactionRunnerUtils::getReactantMatchesToTemplate(RDKit::ROMol const&, RDKit::ROMol const&, unsigned int, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 -95: 19# RDKit::ReactionRunnerUtils::getReactantMatches(std::vector, std::allocator > > const&, RDKit::ChemicalReaction const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >, std::allocator, std::allocator > >, std::allocator, std::allocator > > > > > >&, unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 -95: 20# RDKit::run_Reactants(RDKit::ChemicalReaction const&, std::vector, std::allocator > > const&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 -95: 21# RDKit::ChemicalReaction::runReactants(std::vector, std::allocator > >, unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 -95: 22# _object* RDKit::RunReactants(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -95: 23# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -95: 24# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -95: 25# 0x0000FFFFBCC315C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -95: 26# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -95: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so -95: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so -95: 29# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -95: 30# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -95: 31# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so -95: 32# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -95: 33# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -95: 34# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -95: 35# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -95: 36# 0x0000FFFFBA714180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -95: 37# 0x0000FFFFBA714118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -95: 38# 0x0000FFFFBA7140A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -95: 39# 0x0000FFFFBA714040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -95: 40# 0x0000FFFFBA713FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -95: 41# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so -95: 42# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so -95: 43# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so -95: 44# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so -95: 45# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -95: 46# 0x0000FFFFBCC2E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -95: 47# _PyObject_MakeTpCall in /usr/bin/python3 -95: 48# _PyEval_EvalFrameDefault in /usr/bin/python3 -95: 49# 0x00000000004C3D1C in /usr/bin/python3 -95: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 -95: 51# _PyObject_Call_Prepend in /usr/bin/python3 -95: 52# 0x000000000052608C in /usr/bin/python3 -95: 53# _PyObject_MakeTpCall in /usr/bin/python3 -95: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 -95: 55# 0x00000000004C3D1C in /usr/bin/python3 -95: 56# _PyEval_EvalFrameDefault in /usr/bin/python3 -95: 57# _PyObject_Call_Prepend in /usr/bin/python3 -95: 58# 0x000000000052608C in /usr/bin/python3 -95: 59# _PyObject_MakeTpCall in /usr/bin/python3 -95: 60# _PyEval_EvalFrameDefault in /usr/bin/python3 -95: 61# 0x00000000004C3D1C in /usr/bin/python3 -95: 62# _PyEval_EvalFrameDefault in /usr/bin/python3 -95: 63# _PyObject_Call_Prepend in /usr/bin/python3 -95: 64# 0x000000000052608C in /usr/bin/python3 -95: 65# _PyObject_MakeTpCall in /usr/bin/python3 -95: 66# _PyEval_EvalFrameDefault in /usr/bin/python3 -95: 67# _PyObject_Call_Prepend in /usr/bin/python3 -95: 68# 0x000000000051FB4C in /usr/bin/python3 -95: 69# 0x000000000051B324 in /usr/bin/python3 -95: 70# _PyObject_MakeTpCall in /usr/bin/python3 -95: 71# _PyEval_EvalFrameDefault in /usr/bin/python3 -95: 72# PyEval_EvalCode in /usr/bin/python3 -95: 73# 0x0000000000595200 in /usr/bin/python3 -95: 74# 0x00000000006757AC in /usr/bin/python3 -95: 75# _PyRun_SimpleFileObject in /usr/bin/python3 -95: 76# _PyRun_AnyFileObject in /usr/bin/python3 -95: 77# Py_RunMain in /usr/bin/python3 -95: 78# Py_BytesMain in /usr/bin/python3 -95: 79# 0x0000FFFFBD63229C in /lib/aarch64-linux-gnu/libc.so.6 -95: 80# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -95: 81# _start in /usr/bin/python3 -95: ---------- -95: **** -95: -95: [02:22:50] -95: -95: **** +97: [23:09:41] reactant 0 has no mapped atoms. +97: [23:09:41] reactant 1 has no mapped atoms. +97: [23:09:41] product 0 has no mapped atoms. +97: [23:09:41] Could not find RLabel mapping for atom: 0 in template: 1 +97: [23:09:41] reactant 1 has no mapped atoms. +97: [23:09:41] reactant 1 has no mapped atoms. +97: [23:09:41] reactant 1 has no mapped atoms. 97: .. 97: ---------------------------------------------------------------------- -97: Ran 4 tests in 0.019s +97: Ran 4 tests in 0.057s 97: 97: OK 97: @@ -24361,165 +24376,219 @@ 97: M END 97: 97: $RXN Failed -95: Pre-condition Violation -95: getNumImplicitHs() called without preceding call to calcImplicitValence() -95: Violation occurred on line 302 in file ./Code/GraphMol/Atom.cpp -95: Failed Expression: d_implicitValence > -1 -95: ---------- -95: Stacktrace: -95: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -95: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -95: 2# RDKit::Atom::getNumImplicitHs() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -95: 3# RDKit::Atom::getTotalNumHs(bool) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -95: 4# Queries::EqualityQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 -95: 5# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -95: 6# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -95: 7# Queries::OrQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -95: 8# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -95: 9# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -95: 10# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -95: 11# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -95: 12# RDKit::detail::RecursiveMatcher(RDKit::ROMol const&, RDKit::ROMol const&, std::vector >&, std::map*, std::less, std::allocator*> > >&, RDKit::SubstructMatchParameters const&, std::vector >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -95: 13# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -95: 14# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -95: 15# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -95: 16# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -95: 17# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -95: 18# RDKit::ReactionRunnerUtils::getReactantMatchesToTemplate(RDKit::ROMol const&, RDKit::ROMol const&, unsigned int, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 -95: 19# RDKit::ReactionRunnerUtils::getReactantMatches(std::vector, std::allocator > > const&, RDKit::ChemicalReaction const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >, std::allocator, std::allocator > >, std::allocator, std::allocator > > > > > >&, unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 -95: 20# RDKit::run_Reactants(RDKit::ChemicalReaction const&, std::vector, std::allocator > > const&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 -95: 21# RDKit::ChemicalReaction::runReactants(std::vector, std::allocator > >, unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 -95: 22# _object* RDKit::RunReactants(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -95: 23# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -95: 24# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -95: 25# 0x0000FFFFBCC315C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -95: 26# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -95: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so -95: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so -95: 29# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -95: 30# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -95: 31# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so -95: 32# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -95: 33# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -95: 34# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -95: 35# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -95: 36# 0x0000FFFFBA714180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -95: 37# 0x0000FFFFBA714118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -95: 38# 0x0000FFFFBA7140A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -95: 39# 0x0000FFFFBA714040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -95: 40# 0x0000FFFFBA713FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -95: 41# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so -95: 42# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so -95: 43# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so -95: 44# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so -95: 45# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -95: 46# 0x0000FFFFBCC2E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -95: 47# _PyObject_MakeTpCall in /usr/bin/python3 -95: 48# _PyEval_EvalFrameDefault in /usr/bin/python3 -95: 49# 0x00000000004C3D1C in /usr/bin/python3 -95: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 -95: 51# _PyObject_Call_Prepend in /usr/bin/python3 -95: 52# 0x000000000052608C in /usr/bin/python3 -95: 53# _PyObject_MakeTpCall in /usr/bin/python3 -95: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 -95: 55# 0x00000000004C3D1C in /usr/bin/python3 -95: 56# _PyEval_EvalFrameDefault in /usr/bin/python3 -95: 57# _PyObject_Call_Prepend in /usr/bin/python3 -95: 58# 0x000000000052608C in /usr/bin/python3 -95: 59# _PyObject_MakeTpCall in /usr/bin/python3 -95: 60# _PyEval_EvalFrameDefault in /usr/bin/python3 -95: 61# 0x00000000004C3D1C in /usr/bin/python3 -95: 62# _PyEval_EvalFrameDefault in /usr/bin/python3 -95: 63# _PyObject_Call_Prepend in /usr/bin/python3 -95: 64# 0x000000000052608C in /usr/bin/python3 -95: 65# _PyObject_MakeTpCall in /usr/bin/python3 -95: 66# _PyEval_EvalFrameDefault in /usr/bin/python3 -95: 67# _PyObject_Call_Prepend in /usr/bin/python3 -95: 68# 0x000000000051FB4C in /usr/bin/python3 -95: 69# 0x000000000051B324 in /usr/bin/python3 -95: 70# _PyObject_MakeTpCall in /usr/bin/python3 -95: 71# _PyEval_EvalFrameDefault in /usr/bin/python3 -95: 72# PyEval_EvalCode in /usr/bin/python3 -95: 73# 0x0000000000595200 in /usr/bin/python3 -95: 74# 0x00000000006757AC in /usr/bin/python3 -95: 75# _PyRun_SimpleFileObject in /usr/bin/python3 -95: 76# _PyRun_AnyFileObject in /usr/bin/python3 -95: 77# Py_RunMain in /usr/bin/python3 -95: 78# Py_BytesMain in /usr/bin/python3 -95: 79# 0x0000FFFFBD63229C in /lib/aarch64-linux-gnu/libc.so.6 -95: 80# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -95: 81# _start in /usr/bin/python3 -95: ---------- -95: **** -95: -95: .........[02:22:50] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -95: [02:22:50] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -95: [02:22:50] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -95: [02:22:50] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -95: .[02:22:50] product atom-mapping number 1 found multiple times. -95: [02:22:50] product atom-mapping number 1 found multiple times. -95: ................[02:22:50] mapped atoms in the reactants were not mapped in the products. -95: unmapped numbers are: 3 -95: [02:22:50] mapped atoms in the reactants were not mapped in the products. -95: unmapped numbers are: 3 -96: [02:22:50] == testCartesianProduct -95: .[02:22:50] mapped atoms in the reactants were not mapped in the products. -95: unmapped numbers are: 3 -95: ..[02:22:50] reactant 2 has no mapped atoms. -95: [02:22:50] reactant 2 has no mapped atoms. -95: [02:22:50] product 1 has no mapped atoms. -100: Randomness seeded to: 1376698797 -100: =============================================================================== -100: All tests passed (93 assertions in 13 test cases) -100: - 89/230 Test #97: pyChemReactionSanitize ................. Passed 0.51 sec - 90/230 Test #100: tautomerQueryTestCatch ................. Passed 0.12 sec + 87/230 Test #98: testChemTransforms ..................... Passed 0.22 sec +test 99 + Start 99: chemTransformsTestCatch + +99: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms +99: Test timeout computed to be: 1500 +99: Randomness seeded to: 695862591 +99: [23:09:41] Incomplete atom labelling, cannot make bond +99: [23:09:41] +99: +99: **** +99: Invariant Violation +99: molzip: bond info already exists for end atom with label:1 +99: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +99: Failed Expression: !bond.b +99: ---------- +99: Stacktrace: +99: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +99: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +99: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 +99: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 +99: 4# 0x0000AAAABFC569A0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 5# 0x0000AAAABFCA5A4C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 6# 0x0000AAAABFCA6400 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 7# 0x0000AAAABFCA6834 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 8# 0x0000AAAABFC7AEF8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 9# 0x0000AAAABFC7B444 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 10# 0x0000AAAABFC4BE90 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 11# 0x0000FFFFB810229C in /lib/aarch64-linux-gnu/libc.so.6 +99: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +99: 13# 0x0000AAAABFC4BF70 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: ---------- +99: **** +99: +99: [23:09:41] Incomplete atom labelling, cannot make bond +99: [23:09:41] +99: +99: **** +99: Invariant Violation +99: molzip: bond info already exists for end atom with label:1 +99: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +99: Failed Expression: !bond.b +99: ---------- +99: Stacktrace: +99: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +99: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +99: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 +99: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 +99: 4# 0x0000AAAABFC569A0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 5# 0x0000AAAABFCA5A4C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 6# 0x0000AAAABFCA6400 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 7# 0x0000AAAABFCA6834 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 8# 0x0000AAAABFC7AEF8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 9# 0x0000AAAABFC7B444 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 10# 0x0000AAAABFC4BE90 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 11# 0x0000FFFFB810229C in /lib/aarch64-linux-gnu/libc.so.6 +99: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +99: 13# 0x0000AAAABFC4BF70 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: ---------- +99: **** +99: +99: [23:09:41] Incomplete atom labelling, cannot make bond +99: [23:09:41] +99: +99: **** +99: Invariant Violation +99: molzip: bond info already exists for end atom with label:1 +99: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +99: Failed Expression: !bond.b +99: ---------- +99: Stacktrace: +99: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +99: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +99: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 +99: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 +99: 4# 0x0000AAAABFC569A0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 5# 0x0000AAAABFCA5A4C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 6# 0x0000AAAABFCA6400 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 7# 0x0000AAAABFCA6834 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 8# 0x0000AAAABFC7AEF8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 9# 0x0000AAAABFC7B444 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 10# 0x0000AAAABFC4BE90 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 11# 0x0000FFFFB810229C in /lib/aarch64-linux-gnu/libc.so.6 +99: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +99: 13# 0x0000AAAABFC4BF70 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: ---------- +99: **** +99: +99: [23:09:41] Incomplete atom labelling, cannot make bond +99: [23:09:41] Incomplete atom labelling, cannot make bond +99: [23:09:41] Incomplete atom labelling, cannot make bond +99: [23:09:41] +99: +99: **** +99: Invariant Violation +99: molzip: bond info already exists for end atom with label:1 +99: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +99: Failed Expression: !bond.b +99: ---------- +99: Stacktrace: +99: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +99: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +99: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 +99: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 +99: 4# 0x0000AAAABFC569A0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 5# 0x0000AAAABFCA5A4C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 6# 0x0000AAAABFCA6400 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 7# 0x0000AAAABFCA6834 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 8# 0x0000AAAABFC7AEF8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 9# 0x0000AAAABFC7B444 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 10# 0x0000AAAABFC4BE90 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 11# 0x0000FFFFB810229C in /lib/aarch64-linux-gnu/libc.so.6 +99: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +99: 13# 0x0000AAAABFC4BF70 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: ---------- +99: **** +99: +99: [23:09:41] Incomplete atom labelling, cannot make bond +99: [23:09:41] +99: +99: **** +99: Invariant Violation +99: molzip: bond info already exists for end atom with label:1 +99: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +99: Failed Expression: !bond.b +99: ---------- +99: Stacktrace: +99: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +99: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +99: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 +99: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 +99: 4# 0x0000AAAABFC569A0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 5# 0x0000AAAABFCA5A4C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 6# 0x0000AAAABFCA6400 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 7# 0x0000AAAABFCA6834 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 8# 0x0000AAAABFC7AEF8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 9# 0x0000AAAABFC7B444 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 10# 0x0000AAAABFC4BE90 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 11# 0x0000FFFFB810229C in /lib/aarch64-linux-gnu/libc.so.6 +99: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +99: 13# 0x0000AAAABFC4BF70 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: ---------- +99: **** +99: +99: [23:09:41] +99: +99: **** +99: Invariant Violation +99: molzip: zipped Bond already exists, perhaps labels are duplicated +99: Violation occurred on line 742 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +99: Failed Expression: params.label == MolzipLabel::FragmentOnBonds || !a->getOwningMol().getBondBetweenAtoms(a->getIdx(), b->getIdx()) +99: ---------- +99: Stacktrace: +99: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +99: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +99: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 +99: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 +99: 4# RDKit::molzip(RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 +99: 5# 0x0000AAAABFC4CC58 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 6# 0x0000AAAABFCA5A4C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 7# 0x0000AAAABFCA6400 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 8# 0x0000AAAABFCA6834 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 9# 0x0000AAAABFC7AEF8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 10# 0x0000AAAABFC7B444 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 11# 0x0000AAAABFC4BE90 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: 12# 0x0000FFFFB810229C in /lib/aarch64-linux-gnu/libc.so.6 +99: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +99: 14# 0x0000AAAABFC4BF70 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +99: ---------- +99: **** +99: +99: =============================================================================== +99: All tests passed (674 assertions in 9 test cases) +99: + 88/230 Test #99: chemTransformsTestCatch ................ Passed 0.24 sec +test 100 + Start 100: tautomerQueryTestCatch + +100: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch +100: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery +100: Test timeout computed to be: 1500 +87: [23:09:41] Explicit valence for atom # 2 O, 4, is greater than permitted +87: [23:09:41] Explicit valence for atom # 3 Al, 6, is greater than permitted +87: [23:09:41] Explicit valence for atom # 3 Be, 4, is greater than permitted + 89/230 Test #97: pyChemReactionSanitize ................. Passed 1.40 sec test 101 Start 101: pyTautomerQuery 101: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/TautomerQuery/Wrap/rough_test.py" 101: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap 101: Test timeout computed to be: 1500 +87: [23:09:41] Explicit valence for atom # 27 P, 6, is greater than permitted +87: =============================================================================== +87: All tests passed (21162 assertions in 3 test cases) +87: + 90/230 Test #87: multithreadedSupplierCatchTest ......... Passed 5.52 sec test 102 Start 102: testSubgraphs1 102: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs1 102: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs 102: Test timeout computed to be: 1500 -95: ........[02:22:50] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q -95: [02:22:50] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' -95: [02:22:50] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q -95: [02:22:50] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' -95: .[02:22:50] reactant atom-mapping number 1 found multiple times. -95: [02:22:50] product atom-mapping number 2 not found in reactants. -95: [02:22:50] mapped atoms in the reactants were not mapped in the products. -95: unmapped numbers are: 4 -95: [02:22:50] product atom-mapping number 5 not found in reactants. -96: .[02:22:50] == testEnumerateLibrary 102: ----------------------- 102: Subgraph retrieval 102: Finished 102: ----------------------- 102: testSubgraphs2a 102: Finished +27: Checking against /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 102: ----------------------- 102: testSubgraphs2 -96: /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py:266: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/testData/enumeration.pickle'> -96: open(os.path.join(self.dataDir, "enumeration.pickle"), 'rb').read()) -96: ResourceWarning: Enable tracemalloc to get the object allocation traceback -95: ........./build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:745: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/testData/reaction1.no_metadata.png'> -95: png = open(fname, 'rb').read() -95: ResourceWarning: Enable tracemalloc to get the object allocation traceback -95: [02:22:50] Found a SCD/SED line with missing/empty SDT specification at line 34 -95: [02:22:50] Found a SCD/SED line with missing/empty SDT specification at line 36 -95: [02:22:50] Found a SCD/SED line with missing/empty SDT specification at line 38 -95: [02:22:50] Found a SCD/SED line with missing/empty SDT specification at line 40 -95: [02:22:50] Found a SCD/SED line with missing/empty SDT specification at line 42 -95: [02:22:50] Found a SCD/SED line with missing/empty SDT specification at line 87 -95: [02:22:50] Found a SCD/SED line with missing/empty SDT specification at line 89 -95: [02:22:50] Found a SCD/SED line with missing/empty SDT specification at line 91 -95: [02:22:50] Found a SCD/SED line with missing/empty SDT specification at line 93 -95: [02:22:50] Found a SCD/SED line with missing/empty SDT specification at line 95 +27: All 191 tests passed 102: Finished 102: ----------------------- 102: Path retrieval @@ -24532,62 +24601,13 @@ 102: Finished 102: ----------------------- 102: testUniqueSubgraphs2 -96: ..[02:22:50] == testRGroupState -96: .[02:22:50] == testRandomEnumerateAllBBsLibrary -96: ** [1, 1] -96: ** [0, 2] -96: ** [1, 0] -96: .[02:22:50] == testRandomEnumerateLibrary -96: .[02:22:50] == testRandomSample -96: .[02:22:50] == testRandomSampleAllBBs -96: .[02:22:50] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -96: [02:22:50] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -101: ..... -101: ---------------------------------------------------------------------- -101: Ran 5 tests in 0.030s -101: -101: OK -96: .[02:22:50] == testRemoveBadMatches -96: .[02:22:50] == testTimings -95: ..[02:22:50] SMARTS Parse Error: syntax error while parsing: boromicacid -95: [02:22:50] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -95: [02:22:50] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -95: [02:22:50] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -95: [02:22:50] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -95: [02:22:50] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -95: [02:22:50] reaction has no reactants -95: [02:22:50] reaction has no products -95: [02:22:50] initialization failed -95: [02:22:50] reaction has no reactants -95: [02:22:50] reaction has no products -95: .[02:22:50] SMARTS Parse Error: syntax error while parsing: boromicacid -95: [02:22:50] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -95: [02:22:50] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -95: [02:22:50] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -87: [02:22:50] Explicit valence for atom # 9 N, 6, is greater than permitted -95: [02:22:50] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -95: [02:22:50] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -95: [02:22:50] reaction has no reactants -95: [02:22:50] reaction has no products -95: [02:22:50] initialization failed -95: [02:22:50] reaction has no reactants -95: [02:22:50] reaction has no products -95: . -95: ---------------------------------------------------------------------- -95: Ran 54 tests in 0.444s -95: -95: OK -95: ******************************************** -95: /build/reproducible-path/rdkit-202409.2/Code/GraphMol/ChemReactions/testData/AmideBond.rxn -95: -102: Finished -102: ----------------------- -102: testRootedSubgraphs -102: Finished -102: ----------------------- -102: testRootedPaths -102: Finished - 91/230 Test #102: testSubgraphs1 ......................... Passed 0.33 sec +27: +27: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... +100: Randomness seeded to: 625784484 +100: =============================================================================== +100: All tests passed (93 assertions in 13 test cases) +100: + 91/230 Test #100: tautomerQueryTestCatch ................. Passed 0.57 sec test 103 Start 103: testSubgraphs2 @@ -24605,48 +24625,43 @@ 103: Finished 103: ----------------------- 103: Testing github Issue103: stereochemistry and pathToSubmol - 92/230 Test #101: pyTautomerQuery ........................ Passed 0.37 sec +103: Finished +103: ----------------------- +103: Testing github Issue103: more stereochemistry and pathToSubmol (path needs to be in sorted order) +103: Finished + 92/230 Test #103: testSubgraphs2 ......................... Passed 0.09 sec test 104 Start 104: subgraphsCatch 104: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/subgraphsCatch 104: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs 104: Test timeout computed to be: 1500 -103: Finished -103: ----------------------- -103: Testing github Issue103: more stereochemistry and pathToSubmol (path needs to be in sorted order) -103: Finished - 93/230 Test #103: testSubgraphs2 ......................... Passed 0.05 sec +104: Randomness seeded to: 2793178470 +104: --------- +104: =============================================================================== +104: All tests passed (11 assertions in 1 test case) +104: + 93/230 Test #104: subgraphsCatch ......................... Passed 0.04 sec test 105 Start 105: filterCatalogTest 105: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/filterCatalogTest 105: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog 105: Test timeout computed to be: 1500 -87: [02:22:50] Explicit valence for atom # 3 Al, 6, is greater than permitted - 94/230 Test #95: pyChemReactions ........................ Passed 1.16 sec +102: Finished +102: ----------------------- +102: testRootedSubgraphs +102: Finished +102: ----------------------- +102: testRootedPaths +102: Finished + 94/230 Test #102: testSubgraphs1 ......................... Passed 0.62 sec test 106 Start 106: pyFilterCatalog 106: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/FilterCatalog/Wrap/rough_test.py" 106: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap 106: Test timeout computed to be: 1500 -104: Randomness seeded to: 3677446499 -104: --------- -104: =============================================================================== -104: All tests passed (11 assertions in 1 test case) -104: - 95/230 Test #104: subgraphsCatch ......................... Passed 0.05 sec -test 107 - Start 107: testFragCatalog - -107: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -107: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog -107: Test timeout computed to be: 1500 -27: Checking against /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -87: [02:22:50] Explicit valence for atom # 4 Al, 6, is greater than permitted -87: [02:22:50] Explicit valence for atom # 10 Si, 6, is greater than permitted -107: 21 105: Warning: molecule failed filter 105: Warning: molecule failed filter: reason hzone_phenol_A(479) 105: v = { @@ -24735,75 +24750,106 @@ 105: 10,15}, 105: 11,16}, 105: } -87: [02:22:50] Explicit valence for atom # 2 O, 4, is greater than permitted -87: [02:22:50] Explicit valence for atom # 3 Al, 6, is greater than permitted -87: [02:22:50] Explicit valence for atom # 3 Be, 4, is greater than permitted -87: [02:22:50] Explicit valence for atom # 27 P, 6, is greater than permitted -87: =============================================================================== -87: All tests passed (21162 assertions in 3 test cases) -87: - 96/230 Test #87: multithreadedSupplierCatchTest ......... Passed 2.15 sec +101: ..... +101: ---------------------------------------------------------------------- +101: Ran 5 tests in 0.114s +101: +101: OK + 95/230 Test #105: filterCatalogTest ...................... Passed 0.48 sec +test 107 + Start 107: testFragCatalog + +107: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +107: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog +107: Test timeout computed to be: 1500 +107: 21 + 96/230 Test #101: pyTautomerQuery ........................ Passed 1.34 sec test 108 Start 108: pyFragCatalog 108: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/FragCatalog/Wrap/rough_test.py" 108: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap 108: Test timeout computed to be: 1500 -27: All 191 tests passed - 97/230 Test #105: filterCatalogTest ...................... Passed 0.29 sec +96: . +96: ---------------------------------------------------------------------- +96: Ran 11 tests in 2.438s +96: +96: OK +96: True +96: == CartesianProductStrategy CartesianProductStrategy +96: 197 out of 300 +96: 0 6 out of 10 +96: 1 3 out of 5 +96: 2 4 out of 6 +96: 198 out of 300 +96: 0 10 out of 10 +96: 1 5 out of 5 +96: 2 6 out of 6 +96: Skipped 10000000 in 0.16218161582946777 seconds +96: Skipped 10000000 in 1.2756521701812744 seconds +96: Skipped 10000000 in 0.3743410110473633 seconds + 97/230 Test #96: pyChemReactionEnumerations ............. Passed 3.62 sec test 109 Start 109: testDescriptors 109: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testDescriptors 109: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 109: Test timeout computed to be: 1500 -109: [02:22:51] ------------------------------------- -109: [02:22:51] Test Crippen parameter acquisition. -109: [02:22:51] done -109: [02:22:51] ------------------------------------- -109: [02:22:51] Test Crippen calculation. -109: [02:22:51] done -109: [02:22:51] ------------------------------------- -109: [02:22:51] Test Issue262: problems with Crippen calculation from pickles. -109: [02:22:51] done -109: [02:22:51] ------------------------------------- -109: [02:22:51] Test AMW calculation. -109: [02:22:51] done -109: [02:22:51] ------------------------------------- -109: [02:22:51] Test Exact MW calculation. -109: [02:22:51] done -109: [02:22:51] ------------------------------------- -109: [02:22:51] Test Labute ASA descriptors. -109: [02:22:51] done -109: [02:22:51] ------------------------------------- -109: [02:22:51] Test TPSA descriptors. -109: [02:22:51] done -109: [02:22:51] ------------------------------------- -109: [02:22:51] Test Lipinski parameters. -109: [02:22:51] done -109: [02:22:51] ------------------------------------- -109: [02:22:51] Test VSA descriptors. -109: [02:22:51] done -109: [02:22:51] ------------------------------------- -109: [02:22:51] Test molecular formula calculation. -109: [02:22:51] done -109: [02:22:51] ------------------------------------- -109: [02:22:51] Test Issue 3415534. -109: [02:22:51] done -109: [02:22:51] ------------------------------------- -109: [02:22:51] Test Issue3433771: Bad definition for Crippen atom type O11. -109: [02:22:51] done -109: [02:22:51] ------------------------------------- -109: [02:22:51] Test multithreading +109: [23:09:43] ------------------------------------- +109: [23:09:43] Test Crippen parameter acquisition. +109: [23:09:43] done +109: [23:09:43] ------------------------------------- +109: [23:09:43] Test Crippen calculation. +109: [23:09:43] done +109: [23:09:43] ------------------------------------- +109: [23:09:43] Test Issue262: problems with Crippen calculation from pickles. +109: [23:09:43] done +109: [23:09:43] ------------------------------------- +109: [23:09:43] Test AMW calculation. +109: [23:09:43] done +109: [23:09:43] ------------------------------------- +109: [23:09:43] Test Exact MW calculation. +109: [23:09:43] done +109: [23:09:43] ------------------------------------- +109: [23:09:43] Test Labute ASA descriptors. +109: [23:09:43] done +109: [23:09:43] ------------------------------------- +109: [23:09:43] Test TPSA descriptors. +109: [23:09:43] done +109: [23:09:43] ------------------------------------- +109: [23:09:43] Test Lipinski parameters. +109: [23:09:43] done +109: [23:09:43] ------------------------------------- +109: [23:09:43] Test VSA descriptors. +109: [23:09:43] done +109: [23:09:43] ------------------------------------- +109: [23:09:43] Test molecular formula calculation. +109: [23:09:43] done +109: [23:09:43] ------------------------------------- +109: [23:09:43] Test Issue 3415534. +109: [23:09:43] done +109: [23:09:43] ------------------------------------- +109: [23:09:43] Test Issue3433771: Bad definition for Crippen atom type O11. +109: [23:09:43] done +109: [23:09:43] ------------------------------------- +109: [23:09:43] Test multithreading 109: reading molecules +73: [23:09:43] Finished: testSmiCorrectness() +73: [23:09:43] ----------------------------------------- +73: +73: [23:09:43] +73: ----------------------------------------- 109: processing 109: launch :0 109: launch :1 109: launch :2 109: launch :3 -27: -27: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... -107: [02:22:51] +108: ......... +108: ---------------------------------------------------------------------- +108: Ran 9 tests in 0.105s +108: +108: OK +107: [23:09:43] 107: 107: **** 107: Invariant Violation @@ -24814,17 +24860,17 @@ 107: Stacktrace: 107: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 107: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -107: 2# 0x0000FFFFAA871910 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 +107: 2# 0x0000FFFFB9FB1910 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 107: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 -107: 4# 0x0000AAAAD190785C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -107: 5# 0x0000AAAAD1904760 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -107: 6# 0x0000FFFFA9E5229C in /lib/aarch64-linux-gnu/libc.so.6 +107: 4# 0x0000AAAAD34F785C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +107: 5# 0x0000AAAAD34F4760 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +107: 6# 0x0000FFFFB959229C in /lib/aarch64-linux-gnu/libc.so.6 107: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -107: 8# 0x0000AAAAD1904930 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +107: 8# 0x0000AAAAD34F4930 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 107: ---------- 107: **** 107: -107: [02:22:51] +107: [23:09:43] 107: 107: **** 107: Invariant Violation @@ -24835,17 +24881,17 @@ 107: Stacktrace: 107: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 107: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -107: 2# 0x0000FFFFAA871910 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 +107: 2# 0x0000FFFFB9FB1910 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 107: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 -107: 4# 0x0000AAAAD190785C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -107: 5# 0x0000AAAAD1904760 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -107: 6# 0x0000FFFFA9E5229C in /lib/aarch64-linux-gnu/libc.so.6 +107: 4# 0x0000AAAAD34F785C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +107: 5# 0x0000AAAAD34F4760 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +107: 6# 0x0000FFFFB959229C in /lib/aarch64-linux-gnu/libc.so.6 107: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -107: 8# 0x0000AAAAD1904930 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +107: 8# 0x0000AAAAD34F4930 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 107: ---------- 107: **** 107: -107: [02:22:51] +107: [23:09:43] 107: 107: **** 107: Invariant Violation @@ -24856,169 +24902,368 @@ 107: Stacktrace: 107: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 107: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -107: 2# 0x0000FFFFAA871910 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 +107: 2# 0x0000FFFFB9FB1910 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 107: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 -107: 4# 0x0000AAAAD190785C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -107: 5# 0x0000AAAAD1904760 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -107: 6# 0x0000FFFFA9E5229C in /lib/aarch64-linux-gnu/libc.so.6 +107: 4# 0x0000AAAAD34F785C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +107: 5# 0x0000AAAAD34F4760 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +107: 6# 0x0000FFFFB959229C in /lib/aarch64-linux-gnu/libc.so.6 107: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -107: 8# 0x0000AAAAD1904930 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +107: 8# 0x0000AAAAD34F4930 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 107: ---------- 107: **** 107: - 98/230 Test #107: testFragCatalog ........................ Passed 0.65 sec + 98/230 Test #107: testFragCatalog ........................ Passed 1.07 sec test 110 Start 110: testAUTOCORR2D 110: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR2D 110: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 110: Test timeout computed to be: 1500 -110: [02:22:51] ---------------------------- +73: [23:09:44] Property will be truncated after the first blank line +73: [23:09:44] Property will be truncated after the first blank line +73: [23:09:44] Spurious data before the first property will be ignored +73: [23:09:44] Property will be truncated after the first blank line +110: [23:09:44] ---------------------------- 110: start test autocorr2D -108: ......... -108: ---------------------------------------------------------------------- -108: Ran 9 tests in 0.068s -108: -108: OK - 99/230 Test #108: pyFragCatalog .......................... Passed 0.57 sec + 99/230 Test #108: pyFragCatalog .......................... Passed 0.98 sec test 111 Start 111: testATF 111: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testATF 111: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 111: Test timeout computed to be: 1500 -100/230 Test #111: testATF ................................ Passed 0.04 sec +100/230 Test #111: testATF ................................ Passed 0.05 sec test 112 Start 112: testBCUT 112: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testBCUT 112: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 112: Test timeout computed to be: 1500 -112: [02:22:51] ------------------------------------- -112: [02:22:51] Basic BCUT tests. -112: [02:22:51] done -112: [02:22:51] ------------------------------------- -112: [02:22:51] Larger BCUT tests. -106: .............[02:22:51] SMILES Parse Error: syntax error while parsing: --- -106: [02:22:51] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [02:22:51] dasfsadf -106: [02:22:51] SMILES Parse Error: syntax error while parsing: --- -106: [02:22:51] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [02:22:51] dasfsadf -106: [02:22:51] SMILES Parse Error: syntax error while parsing: --- -106: [02:22:51] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [02:22:51] dasfsadf -106: [02:22:51] SMILES Parse Error: syntax error while parsing: --- -106: [02:22:51] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [02:22:51] dasfsadf -106: [02:22:51] SMILES Parse Error: syntax error while parsing: --- -106: [02:22:51] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [02:22:51] dasfsadf -106: [02:22:51] SMILES Parse Error: syntax error while parsing: --- -106: [02:22:51] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [02:22:51] dasfsadf -106: [02:22:51] SMILES Parse Error: syntax error while parsing: --- -106: [02:22:51] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [02:22:51] dasfsadf -106: [02:22:51] SMILES Parse Error: syntax error while parsing: --- -106: [02:22:51] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [02:22:51] dasfsadf -106: [02:22:51] SMILES Parse Error: syntax error while parsing: --- -106: [02:22:51] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [02:22:51] dasfsadf -106: [02:22:51] SMILES Parse Error: syntax error while parsing: --- -106: [02:22:51] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [02:22:51] dasfsadf -106: [02:22:51] SMILES Parse Error: syntax error while parsing: --- -106: [02:22:51] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [02:22:51] dasfsadf -106: [02:22:51] SMILES Parse Error: syntax error while parsing: --- -106: [02:22:51] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [02:22:51] dasfsadf -106: [02:22:51] SMILES Parse Error: syntax error while parsing: --- -106: [02:22:51] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [02:22:51] dasfsadf -106: [02:22:51] SMILES Parse Error: syntax error while parsing: --- -106: [02:22:51] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [02:22:51] dasfsadf -106: [02:22:51] SMILES Parse Error: syntax error while parsing: --- -106: [02:22:51] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [02:22:51] dasfsadf -106: [02:22:51] SMILES Parse Error: syntax error while parsing: --- -106: [02:22:51] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [02:22:51] dasfsadf -106: [02:22:51] SMILES Parse Error: syntax error while parsing: --- -106: [02:22:51] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [02:22:51] dasfsadf -106: [02:22:51] SMILES Parse Error: syntax error while parsing: --- -106: [02:22:51] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [02:22:51] dasfsadf -106: [02:22:51] SMILES Parse Error: syntax error while parsing: --- -106: [02:22:51] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [02:22:51] dasfsadf -106: [02:22:51] SMILES Parse Error: syntax error while parsing: --- -106: [02:22:51] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [02:22:51] dasfsadf -106: [02:22:51] SMILES Parse Error: syntax error while parsing: --- -106: [02:22:51] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [02:22:51] dasfsadf -106: [02:22:51] SMILES Parse Error: syntax error while parsing: --- -106: [02:22:51] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [02:22:51] dasfsadf -106: [02:22:51] SMILES Parse Error: syntax error while parsing: --- -106: [02:22:51] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [02:22:51] dasfsadf -106: [02:22:51] SMILES Parse Error: syntax error while parsing: --- -106: [02:22:51] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [02:22:51] dasfsadf -106: [02:22:51] SMILES Parse Error: syntax error while parsing: --- -106: [02:22:51] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [02:22:51] dasfsadf -106: [02:22:51] SMILES Parse Error: syntax error while parsing: --- -106: [02:22:51] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [02:22:51] dasfsadf -106: [02:22:51] SMILES Parse Error: syntax error while parsing: --- -106: [02:22:51] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [02:22:51] dasfsadf -106: [02:22:51] SMILES Parse Error: syntax error while parsing: --- -106: [02:22:51] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [02:22:51] dasfsadf -106: [02:22:51] SMILES Parse Error: syntax error while parsing: --- -106: [02:22:51] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [02:22:51] dasfsadf -106: [02:22:51] SMILES Parse Error: syntax error while parsing: --- -106: [02:22:51] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -106: [02:22:51] dasfsadf -96: . -96: ---------------------------------------------------------------------- -96: Ran 11 tests in 1.470s -96: -96: OK -96: True -96: == CartesianProductStrategy CartesianProductStrategy -96: 197 out of 300 -96: 0 6 out of 10 -96: 1 3 out of 5 -96: 2 4 out of 6 -96: 198 out of 300 -96: 0 10 out of 10 -96: 1 5 out of 5 -96: 2 6 out of 6 -96: Skipped 10000000 in 0.08572196960449219 seconds -96: Skipped 10000000 in 0.5779273509979248 seconds -96: Skipped 10000000 in 0.3091883659362793 seconds -106: .[02:22:51] SMILES Parse Error: syntax error while parsing: mydoghasfleas -106: [02:22:51] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' -101/230 Test #96: pyChemReactionEnumerations ............. Passed 2.23 sec +112: [23:09:44] ------------------------------------- +112: [23:09:44] Basic BCUT tests. +112: [23:09:44] done +112: [23:09:44] ------------------------------------- +112: [23:09:44] Larger BCUT tests. +110: [23:09:44] done +110: [23:09:44] ------------------------------------- +110: [23:09:44] Test Github #3806: NaNs from AUTOCORR2D descriptor +110: [23:09:44] done +101/230 Test #110: testAUTOCORR2D ......................... Passed 0.91 sec test 113 Start 113: testEEM 113: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testEEM 113: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 113: Test timeout computed to be: 1500 +113: =>start test EEM +113: [23:09:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: 0 +113: [23:09:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +106: .............[23:09:45] SMILES Parse Error: syntax error while parsing: --- +106: [23:09:45] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [23:09:45] dasfsadf +106: [23:09:45] SMILES Parse Error: syntax error while parsing: --- +106: [23:09:45] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [23:09:45] dasfsadf +106: [23:09:45] SMILES Parse Error: syntax error while parsing: --- +106: [23:09:45] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [23:09:45] dasfsadf +106: [23:09:45] SMILES Parse Error: syntax error while parsing: --- +106: [23:09:45] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [23:09:45] dasfsadf +106: [23:09:45] SMILES Parse Error: syntax error while parsing: --- +106: [23:09:45] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [23:09:45] dasfsadf +106: [23:09:45] SMILES Parse Error: syntax error while parsing: --- +106: [23:09:45] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [23:09:45] dasfsadf +106: [23:09:45] SMILES Parse Error: syntax error while parsing: --- +106: [23:09:45] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [23:09:45] dasfsadf +106: [23:09:45] SMILES Parse Error: syntax error while parsing: --- +106: [23:09:45] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [23:09:45] dasfsadf +106: [23:09:45] SMILES Parse Error: syntax error while parsing: --- +106: [23:09:45] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [23:09:45] dasfsadf +106: [23:09:45] SMILES Parse Error: syntax error while parsing: --- +106: [23:09:45] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [23:09:45] dasfsadf +73: [23:09:45] Finished: testSDCorrectness() +73: [23:09:45] ----------------------------------------- +73: +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +102/230 Test #73: testMultithreadedMolSupplier ........... Passed 10.21 sec +test 114 + Start 114: testPBF + +114: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testPBF +114: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors +114: Test timeout computed to be: 1500 +106: [23:09:45] SMILES Parse Error: syntax error while parsing: --- +106: [23:09:45] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [23:09:45] dasfsadf +106: [23:09:45] SMILES Parse Error: syntax error while parsing: --- +106: [23:09:45] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [23:09:45] dasfsadf +106: [23:09:45] SMILES Parse Error: syntax error while parsing: --- +106: [23:09:45] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [23:09:45] dasfsadf +106: [23:09:45] SMILES Parse Error: syntax error while parsing: --- +106: [23:09:45] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [23:09:45] dasfsadf +106: [23:09:45] SMILES Parse Error: syntax error while parsing: --- +106: [23:09:45] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [23:09:45] dasfsadf +106: [23:09:45] SMILES Parse Error: syntax error while parsing: --- +106: [23:09:45] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [23:09:45] dasfsadf +106: [23:09:45] SMILES Parse Error: syntax error while parsing: --- +106: [23:09:45] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [23:09:45] dasfsadf +106: [23:09:45] SMILES Parse Error: syntax error while parsing: --- +106: [23:09:45] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [23:09:45] dasfsadf +106: [23:09:45] SMILES Parse Error: syntax error while parsing: --- +106: [23:09:45] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [23:09:45] dasfsadf +106: [23:09:45] SMILES Parse Error: syntax error while parsing: --- +106: [23:09:45] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [23:09:45] dasfsadf +106: [23:09:45] SMILES Parse Error: syntax error while parsing: --- +106: [23:09:45] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [23:09:45] dasfsadf +106: [23:09:45] SMILES Parse Error: syntax error while parsing: --- +106: [23:09:45] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [23:09:45] dasfsadf +106: [23:09:45] SMILES Parse Error: syntax error while parsing: --- +106: [23:09:45] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [23:09:45] dasfsadf +106: [23:09:45] SMILES Parse Error: syntax error while parsing: --- +106: [23:09:45] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [23:09:45] dasfsadf +106: [23:09:45] SMILES Parse Error: syntax error while parsing: --- +106: [23:09:45] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [23:09:45] dasfsadf +106: [23:09:45] SMILES Parse Error: syntax error while parsing: --- +106: [23:09:45] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [23:09:45] dasfsadf +106: [23:09:45] SMILES Parse Error: syntax error while parsing: --- +106: [23:09:45] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [23:09:45] dasfsadf +106: [23:09:45] SMILES Parse Error: syntax error while parsing: --- +106: [23:09:45] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [23:09:45] dasfsadf +106: [23:09:45] SMILES Parse Error: syntax error while parsing: --- +106: [23:09:45] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [23:09:45] dasfsadf +106: [23:09:45] SMILES Parse Error: syntax error while parsing: --- +106: [23:09:45] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +106: [23:09:45] dasfsadf +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +114: [23:09:45] ------------------------------------- +114: [23:09:45] Basic PBF tests. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +112: [23:09:45] ------------------------------------- +112: [23:09:45] Test empty molecule BCUT. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103/230 Test #112: testBCUT ............................... Passed 1.00 sec +test 115 + Start 115: testRDFcustom + +115: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testRDFcustom +115: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors +115: Test timeout computed to be: 1500 +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: 100 +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +106: .[23:09:45] SMILES Parse Error: syntax error while parsing: mydoghasfleas +106: [23:09:45] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 106: ....... 106: ---------------------------------------------------------------------- -106: Ran 21 tests in 0.932s +106: Ran 21 tests in 2.196s 106: 106: OK 106: (Five aromatic carbons And (Not any of Five aromatic carbons)) @@ -25040,685 +25285,404 @@ 106: 1 106: 2 106: running -113: =>start test EEM -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: 0 -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -112: [02:22:52] ------------------------------------- -112: [02:22:52] Test empty molecule BCUT. -102/230 Test #112: testBCUT ............................... Passed 0.55 sec -test 114 - Start 114: testPBF - -114: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testPBF -114: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors -114: Test timeout computed to be: 1500 -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103/230 Test #106: pyFilterCatalog ........................ Passed 1.44 sec -test 115 - Start 115: testRDFcustom - -115: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testRDFcustom -115: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors -115: Test timeout computed to be: 1500 -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -114: [02:22:52] ------------------------------------- -114: [02:22:52] Basic PBF tests. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: 100 -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -110: [02:22:52] done -110: [02:22:52] ------------------------------------- -110: [02:22:52] Test Github #3806: NaNs from AUTOCORR2D descriptor -110: [02:22:52] done -114: [02:22:52] done -114: [02:22:52] ------------------------------------- -114: [02:22:52] PBF edge cases. -104/230 Test #110: testAUTOCORR2D ......................... Passed 0.99 sec +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: 200 +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +114: [23:09:45] done +114: [23:09:45] ------------------------------------- +114: [23:09:45] PBF edge cases. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +114: [23:09:45] done +104/230 Test #114: testPBF ................................ Passed 0.53 sec test 116 Start 116: testRDF 116: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testRDF 116: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 116: Test timeout computed to be: 1500 -114: [02:22:52] done -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -105/230 Test #114: testPBF ................................ Passed 0.26 sec +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: 300 +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +105/230 Test #106: pyFilterCatalog ........................ Passed 3.29 sec test 117 Start 117: testMORSE 117: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testMORSE 117: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 117: Test timeout computed to be: 1500 -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: 200 -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: 400 +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: =>start test rdf custom -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [02:22:52] test on : 365 molecules done -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: 300 -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -116: =>start test rdf -116: [02:22:52] test on : 365 molecules done -106/230 Test #116: testRDF ................................ Passed 0.55 sec +115: [23:09:46] test on : 365 molecules done +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: [23:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113: Elapsed time: 1.2235 s +113: Errors:0 +113: [23:09:46] test on : 500 molecules done +106/230 Test #113: testEEM ................................ Passed 1.28 sec test 118 Start 118: test3D 118: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/test3D 118: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 118: Test timeout computed to be: 1500 -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -118: [02:22:52] ------------------------------------- -118: [02:22:52] Basic PMI tests. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: 400 -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -118: [02:22:53] done -118: [02:22:53] ------------------------------------- -118: [02:22:53] More PMI/NPR tests. -118: [02:22:53] done -118: [02:22:53] ------------------------------------- -118: [02:22:53] Basic NPR tests. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: [02:22:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: Elapsed time: 1.38243 s -113: Errors:0 -113: [02:22:53] test on : 500 molecules done -107/230 Test #113: testEEM ................................ Passed 1.41 sec +118: [23:09:46] ------------------------------------- +118: [23:09:46] Basic PMI tests. +116: =>start test rdf +116: [23:09:46] test on : 365 molecules done +107/230 Test #116: testRDF ................................ Passed 1.00 sec test 119 Start 119: testWHIM 119: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testWHIM 119: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 119: Test timeout computed to be: 1500 -118: [02:22:53] done -118: [02:22:53] ------------------------------------- -118: [02:22:53] PMI edge cases. -118: [02:22:53] done -118: [02:22:53] ------------------------------------- -118: [02:22:53] NPR edge cases. -118: [02:22:53] done -118: [02:22:53] ------------------------------------- -118: [02:22:53] 3D descriptors. -118: [02:22:53] done -118: [02:22:53] ------------------------------------- -118: [02:22:53] 3D descriptor edge cases. -118: [02:22:53] done -118: [02:22:53] ------------------------------------- -118: [02:22:53] Inertial shape factor. -118: [02:22:53] done -108/230 Test #118: test3D ................................. Passed 0.40 sec +118: [23:09:46] done +118: [23:09:46] ------------------------------------- +118: [23:09:46] More PMI/NPR tests. +118: [23:09:46] done +118: [23:09:46] ------------------------------------- +118: [23:09:46] Basic NPR tests. +118: [23:09:46] done +118: [23:09:46] ------------------------------------- +118: [23:09:46] PMI edge cases. +118: [23:09:46] done +118: [23:09:46] ------------------------------------- +118: [23:09:46] NPR edge cases. +118: [23:09:46] done +118: [23:09:46] ------------------------------------- +118: [23:09:46] 3D descriptors. +118: [23:09:46] done +118: [23:09:46] ------------------------------------- +118: [23:09:46] 3D descriptor edge cases. +118: [23:09:46] done +118: [23:09:46] ------------------------------------- +118: [23:09:46] Inertial shape factor. +118: [23:09:46] done +108/230 Test #118: test3D ................................. Passed 0.71 sec test 120 Start 120: testGETAWAY 120: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testGETAWAY 120: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 120: Test timeout computed to be: 1500 -115: =>start test morse custom -115: [02:22:53] test on : 365 molecules done -117: =>start test MORSE -117: =>read file -117: [02:22:53] test on : 365 molecules done -109/230 Test #117: testMORSE .............................. Passed 1.13 sec +119: =>start test WHIM +119: [23:09:47] test on : 365 molecules done +109/230 Test #119: testWHIM ............................... Passed 0.82 sec test 121 Start 121: testAUTOCORR3D 121: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR3D 121: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 121: Test timeout computed to be: 1500 -109: [02:22:53] done -109: [02:22:53] ------------------------------------- -109: [02:22:53] Test Issue252: Bad definitions for Crippen atom types. -109: [02:22:53] done -109: [02:22:53] ------------------------------------- -109: [02:22:53] Test calculation of ChiVs. -109: [02:22:53] done -109: [02:22:53] ------------------------------------- -109: [02:22:53] Test calculation of ChiNs. -109: [02:22:53] done -109: [02:22:53] ------------------------------------- -109: [02:22:53] Test calculation of HallKierAlpha. -109: [02:22:53] done -109: [02:22:53] ------------------------------------- -109: [02:22:53] Test calculation of Kappa1. -109: [02:22:53] done -109: [02:22:53] ------------------------------------- -109: [02:22:53] Test calculation of Kappa2. -109: [02:22:53] done -109: [02:22:53] ------------------------------------- -109: [02:22:53] Test calculation of Kappa3. -109: [02:22:53] done -109: [02:22:53] ------------------------------------- -109: [02:22:53] Test Crippen atom type calculations. -109: [02:22:53] done -109: [02:22:53] ------------------------------------- -109: [02:22:53] Test ring descriptors -109: [02:22:53] done -109: [02:22:53] ------------------------------------- -109: [02:22:53] Test other count descriptors. -109: [02:22:53] done -109: [02:22:53] ------------------------------------- -109: [02:22:53] Test MQN -109: [02:22:53] done -109: [02:22:53] ------------------------------------- -109: [02:22:53] Test GitHub Issue 56. -109: [02:22:53] WARNING: not removing hydrogen atom without neighbors -109: [02:22:53] WARNING: not removing hydrogen atom without neighbors -109: [02:22:53] WARNING: not removing hydrogen atom without neighbors -109: [02:22:53] WARNING: not removing hydrogen atom without neighbors -109: [02:22:53] done -109: [02:22:53] ------------------------------------- -109: [02:22:53] Test Github92: Bad Crippen atom type for pyrrole H. -109: [02:22:53] done -109: [02:22:53] ------------------------------------- -109: [02:22:53] Test Github362: order dependence in Kier-Hall descriptors. -109: [02:22:53] done -109: [02:22:53] ------------------------------------- -109: [02:22:53] Test calculation of spiro and bridgehead counts. -109: [02:22:53] done -109: [02:22:53] ------------------------------------- -109: [02:22:53] Test Github694: ExactMolWt ignoring the mass of the electron -109: [02:22:53] done -109: [02:22:53] ------------------------------------- -109: [02:22:53] Testing Properties and KitchenSink -109: [02:22:53] ---Caught keyerror (bad property name)--- -109: [02:22:53] ------------------------------------- -109: [02:22:53] Test USR Descriptor -109: [02:22:53] done -109: [02:22:53] ------------------------------------- -109: [02:22:53] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required -109: [02:22:53] done -109: [02:22:53] ------------------------------------- -109: [02:22:53] Test Github #1973: support P and S terms for TPSA calculation -109: [02:22:53] done -109: [02:22:53] ------------------------------------- -109: [02:22:53] Test Github #2948: Empty molecule has non-zero LabuteASA -109: [02:22:53] done -110/230 Test #109: testDescriptors ........................ Passed 2.68 sec +115: =>start test morse custom +115: [23:09:47] test on : 365 molecules done +117: =>start test MORSE +117: =>read file +117: [23:09:47] test on : 365 molecules done +110/230 Test #117: testMORSE .............................. Passed 2.03 sec test 122 Start 122: testCoulombMat @@ -25727,25 +25691,89 @@ 122: Test timeout computed to be: 1500 122: ===================== Testing CoulombMat ======================= 122: CM test 1 mat Done -111/230 Test #122: testCoulombMat ......................... Passed 0.03 sec +111/230 Test #122: testCoulombMat ......................... Passed 0.11 sec test 123 Start 123: descriptorsTestCatch 123: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/descriptorsTestCatch 123: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 123: Test timeout computed to be: 1500 -119: =>start test WHIM -119: [02:22:53] test on : 365 molecules done -112/230 Test #119: testWHIM ............................... Passed 0.44 sec +109: [23:09:48] done +109: [23:09:48] ------------------------------------- +109: [23:09:48] Test Issue252: Bad definitions for Crippen atom types. +109: [23:09:48] done +109: [23:09:48] ------------------------------------- +109: [23:09:48] Test calculation of ChiVs. +109: [23:09:48] done +109: [23:09:48] ------------------------------------- +109: [23:09:48] Test calculation of ChiNs. +109: [23:09:48] done +109: [23:09:48] ------------------------------------- +109: [23:09:48] Test calculation of HallKierAlpha. +109: [23:09:48] done +109: [23:09:48] ------------------------------------- +109: [23:09:48] Test calculation of Kappa1. +109: [23:09:48] done +109: [23:09:48] ------------------------------------- +109: [23:09:48] Test calculation of Kappa2. +109: [23:09:48] done +109: [23:09:48] ------------------------------------- +109: [23:09:48] Test calculation of Kappa3. +109: [23:09:48] done +109: [23:09:48] ------------------------------------- +109: [23:09:48] Test Crippen atom type calculations. +109: [23:09:48] done +109: [23:09:48] ------------------------------------- +109: [23:09:48] Test ring descriptors +109: [23:09:48] done +109: [23:09:48] ------------------------------------- +109: [23:09:48] Test other count descriptors. +109: [23:09:48] done +109: [23:09:48] ------------------------------------- +109: [23:09:48] Test MQN +109: [23:09:48] done +109: [23:09:48] ------------------------------------- +109: [23:09:48] Test GitHub Issue 56. +109: [23:09:48] WARNING: not removing hydrogen atom without neighbors +109: [23:09:48] WARNING: not removing hydrogen atom without neighbors +109: [23:09:48] WARNING: not removing hydrogen atom without neighbors +109: [23:09:48] WARNING: not removing hydrogen atom without neighbors +109: [23:09:48] done +109: [23:09:48] ------------------------------------- +109: [23:09:48] Test Github92: Bad Crippen atom type for pyrrole H. +109: [23:09:48] done +109: [23:09:48] ------------------------------------- +109: [23:09:48] Test Github362: order dependence in Kier-Hall descriptors. +109: [23:09:48] done +109: [23:09:48] ------------------------------------- +109: [23:09:48] Test calculation of spiro and bridgehead counts. +109: [23:09:48] done +109: [23:09:48] ------------------------------------- +109: [23:09:48] Test Github694: ExactMolWt ignoring the mass of the electron +109: [23:09:48] done +109: [23:09:48] ------------------------------------- +109: [23:09:48] Testing Properties and KitchenSink +109: [23:09:48] ---Caught keyerror (bad property name)--- +109: [23:09:48] ------------------------------------- +109: [23:09:48] Test USR Descriptor +109: [23:09:48] done +109: [23:09:48] ------------------------------------- +109: [23:09:48] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required +109: [23:09:48] done +109: [23:09:48] ------------------------------------- +109: [23:09:48] Test Github #1973: support P and S terms for TPSA calculation +109: [23:09:48] done +109: [23:09:48] ------------------------------------- +109: [23:09:48] Test Github #2948: Empty molecule has non-zero LabuteASA +109: [23:09:48] done +112/230 Test #109: testDescriptors ........................ Passed 4.64 sec test 124 Start 124: pyMolDescriptors 124: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py" 124: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/Wrap 124: Test timeout computed to be: 1500 -115: =>start test AUTOCORR3D custom -115: [02:22:53] test on : 365 molecules done -123: Randomness seeded to: 3411648243 +123: Randomness seeded to: 182380912 123: Warning: Atom Count for residue GLU5A does not match expected count 123: Warning: Atom Count for residue ASN39A does not match expected count 123: Warning: Atom Count for residue GLU53A does not match expected count @@ -25753,147 +25781,31 @@ 123: Warning: Atom Count for residue LYS80A does not match expected count 123: Warning: Atom Count for residue GLU150A does not match expected count 123: Warning: Atom Count for residue ASN157A does not match expected count -73: [02:22:53] Finished: testSmiCorrectness() -73: [02:22:53] ----------------------------------------- -73: -73: [02:22:53] -73: ----------------------------------------- -73: [02:22:54] Spurious data before the first property will be ignored -73: [02:22:54] Property will be truncated after the first blank line -73: [02:22:54] Property will be truncated after the first blank line -73: [02:22:54] Property will be truncated after the first blank line 121: =>start test autocorr3D -121: [02:22:54] test on : 365 molecules done -113/230 Test #121: testAUTOCORR3D ......................... Passed 0.51 sec +121: [23:09:48] test on : 365 molecules done +123: Warning: Atom Count for residue GLU5A does not match expected count +113/230 Test #121: testAUTOCORR3D ......................... Passed 0.97 sec test 125 Start 125: pyMolDescriptors3D 125: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Descriptors/Wrap/test3D.py" 125: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/Wrap 125: Test timeout computed to be: 1500 -123: Warning: Atom Count for residue GLU5A does not match expected count +115: =>start test AUTOCORR3D custom +115: [23:09:48] test on : 365 molecules done +27: Checking against /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 115: =>start test 2 WHIM custom -115: [02:22:54] test on : 365 molecules done -124: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -124: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -124: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -124: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -124: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -124: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -124: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -124: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -124: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -124: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -124: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -124: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -124: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: ..[02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -124: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -124: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -124: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -124: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -124: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -124: .[02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -124: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -124: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -124: ..[02:22:54] -124: -124: **** -124: Pre-condition Violation -124: Number of atom props not equal to number of atoms -124: Violation occurred on line 89 in file ./Code/GraphMol/Descriptors/BCUT.cpp -124: Failed Expression: atom_props.size() == num_atoms -124: ---------- -124: Stacktrace: -124: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -124: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -124: 2# RDKit::Descriptors::BCUT2D(RDKit::ROMol const&, std::vector > const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitDescriptors.so.1 -124: 3# 0x0000FFFFA69AC01C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdMolDescriptors.so -124: 4# 0x0000FFFFA69BF890 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdMolDescriptors.so -124: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -124: 6# 0x0000FFFFAB1B15C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -124: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -124: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so -124: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so -124: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -124: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -124: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so -124: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -124: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -124: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -124: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -124: 17# 0x0000FFFFA8C74180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -124: 18# 0x0000FFFFA8C74118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -124: 19# 0x0000FFFFA8C740A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -124: 20# 0x0000FFFFA8C74040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -124: 21# 0x0000FFFFA8C73FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -124: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so -124: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so -124: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so -124: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so -124: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -124: 27# 0x0000FFFFAB1AE19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -124: 28# _PyObject_MakeTpCall in /usr/bin/python3 -124: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 -124: 30# 0x00000000004C3D1C in /usr/bin/python3 -124: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 -124: 32# _PyObject_Call_Prepend in /usr/bin/python3 -124: 33# 0x000000000052608C in /usr/bin/python3 -124: 34# _PyObject_MakeTpCall in /usr/bin/python3 -124: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 -124: 36# 0x00000000004C3D1C in /usr/bin/python3 -124: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 -124: 38# _PyObject_Call_Prepend in /usr/bin/python3 -124: 39# 0x000000000052608C in /usr/bin/python3 -124: 40# _PyObject_MakeTpCall in /usr/bin/python3 -124: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 -124: 42# 0x00000000004C3D1C in /usr/bin/python3 -124: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 -124: 44# _PyObject_Call_Prepend in /usr/bin/python3 -124: 45# 0x000000000052608C in /usr/bin/python3 -124: 46# _PyObject_MakeTpCall in /usr/bin/python3 -124: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 -124: 48# _PyObject_Call_Prepend in /usr/bin/python3 -124: 49# 0x000000000051FB4C in /usr/bin/python3 -124: 50# 0x000000000051B324 in /usr/bin/python3 -124: 51# _PyObject_MakeTpCall in /usr/bin/python3 -124: 52# _PyEval_EvalFrameDefault in /usr/bin/python3 -124: 53# PyEval_EvalCode in /usr/bin/python3 -124: 54# 0x0000000000595200 in /usr/bin/python3 -124: 55# 0x00000000006757AC in /usr/bin/python3 -124: 56# _PyRun_SimpleFileObject in /usr/bin/python3 -124: 57# _PyRun_AnyFileObject in /usr/bin/python3 -124: 58# Py_RunMain in /usr/bin/python3 -124: 59# Py_BytesMain in /usr/bin/python3 -124: 60# 0x0000FFFFAB9B229C in /lib/aarch64-linux-gnu/libc.so.6 -124: 61# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -124: 62# _start in /usr/bin/python3 -124: ---------- -124: **** -124: -124: ...Warning: Atom Count for residue GLU5A does not match expected count -124: Warning: Atom Count for residue ASN39A does not match expected count -124: Warning: Atom Count for residue GLU53A does not match expected count -124: Warning: Atom Count for residue ARG64A does not match expected count -124: Warning: Atom Count for residue LYS80A does not match expected count -124: Warning: Atom Count for residue GLU150A does not match expected count -124: Warning: Atom Count for residue ASN157A does not match expected count -124: Warning: Atom Count for residue GLU5A does not match expected count -73: [02:22:54] Finished: testSDCorrectness() -73: [02:22:54] ----------------------------------------- -73: -114/230 Test #73: testMultithreadedMolSupplier ........... Passed 6.64 sec +115: [23:09:48] test on : 365 molecules done +27: All 191 tests passed +125: ........ +125: ---------------------------------------------------------------------- +125: Ran 8 tests in 0.250s +125: +125: OK +27: +27: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... +123: Warning: Atom Count for residue ASN39A does not match expected count +114/230 Test #125: pyMolDescriptors3D ..................... Passed 0.89 sec test 126 Start 126: testFingerprints @@ -26383,597 +26295,707 @@ 126: 126: ------------------- 126: -126: [02:22:54] ------------------------------------- -126: [02:22:54] Test Morgan Fingerprints. -126: [02:22:54] done -126: [02:22:54] ------------------------------------- -126: [02:22:54] Test Morgan Fingerprints using fromAtoms argument. -126: [02:22:54] done -126: [02:22:54] ------------------------------------- -126: [02:22:54] Test Morgan Fingerprints as bit vects. -126: [02:22:54] done -126: [02:22:54] ------------------------------------- -126: [02:22:54] Test Morgan Fingerprints with feature invariants. -126: [02:22:54] done -126: [02:22:54] ------------------------------------- -126: [02:22:54] Test additional Morgan fingerprints options. -126: [02:22:54] done -126: [02:22:54] ------------------------------------- -126: [02:22:54] Test Atom Codes. -126: [02:22:54] done -126: [02:22:54] ------------------------------------- -126: [02:22:54] Test Atom Pairs. -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] done -126: [02:22:54] ------------------------------------- -126: [02:22:54] Test Atom Pairs part 2. -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] done -126: [02:22:54] ------------------------------------- -126: [02:22:54] Test Topological Torsions. -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] done -126: [02:22:54] ------------------------------------- -126: [02:22:54] Test Bulk Topological Torsions. -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] ------------------------------------- +126: [23:09:49] Test Morgan Fingerprints. +126: [23:09:49] done +126: [23:09:49] ------------------------------------- +126: [23:09:49] Test Morgan Fingerprints using fromAtoms argument. +126: [23:09:49] done +126: [23:09:49] ------------------------------------- +126: [23:09:49] Test Morgan Fingerprints as bit vects. +126: [23:09:49] done +126: [23:09:49] ------------------------------------- +126: [23:09:49] Test Morgan Fingerprints with feature invariants. +126: [23:09:49] done +126: [23:09:49] ------------------------------------- +126: [23:09:49] Test additional Morgan fingerprints options. +126: [23:09:49] done +126: [23:09:49] ------------------------------------- +126: [23:09:49] Test Atom Codes. +126: [23:09:49] done +126: [23:09:49] ------------------------------------- +126: [23:09:49] Test Atom Pairs. +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] done +126: [23:09:49] ------------------------------------- +126: [23:09:49] Test Atom Pairs part 2. +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] done +126: [23:09:49] ------------------------------------- +126: [23:09:49] Test Topological Torsions. +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] done +126: [23:09:49] ------------------------------------- +126: [23:09:49] Test Bulk Topological Torsions. +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator 115: =>start test 1 WHIM custom -115: [02:22:54] test on : 365 molecules done -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -123: Warning: Atom Count for residue ASN39A does not match expected count -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -125: ........ -125: ---------------------------------------------------------------------- -125: Ran 8 tests in 0.208s -125: -125: OK -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] done -126: [02:22:54] ------------------------------------- -126: [02:22:54] Test Hashed Atom Pairs. -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] done -126: [02:22:54] ------------------------------------- -126: [02:22:54] Test Hashed torsions. -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] done -126: [02:22:54] ------------------------------------- -126: [02:22:54] Test Rooted Atom Pairs. -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] done -126: [02:22:54] ------------------------------------- -126: [02:22:54] Test ignoring atoms in Atom Pairs. -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] done -126: [02:22:54] ------------------------------------- -126: [02:22:54] Test Rooted Topological Torsions. -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] done -126: [02:22:54] ------------------------------------- -126: [02:22:54] Test ignoring atoms in Topological Torsions. -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] done -126: [02:22:54] ------------------------------------- -126: [02:22:54] Test atom info from morgan fingerprints. -126: [02:22:54] done -126: [02:22:54] ------------------------------------- -126: [02:22:54] Test atom info from morgan fingerprints including Info Redundant Environments. -126: [02:22:54] done -126: [02:22:54] ------------------------------------- -126: [02:22:54] ------------------------------------- -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] ------------------------------------- -126: [02:22:54] ------------------------------------- -126: [02:22:54] ------------------------------------- -126: [02:22:54] ------------------------------------- -126: [02:22:54] Test Atom Pairs including info about chirality. -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] done -126: [02:22:54] ------------------------------------- -126: [02:22:54] Test Topological Torsions including info about chirality. -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] done -126: [02:22:54] ------------------------------------- -126: [02:22:54] Test GitHub Issue 25: fingerprint backwards compatibility. -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] done -126: [02:22:54] ------------------------------------- -126: [02:22:54] Test GitHub Issue 151: PatternFingerprint problems -126: [02:22:54] done -126: [02:22:54] ------------------------------------- -126: [02:22:54] Test 3D atom pairs. -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:54] done -126: [02:22:54] ------------------------------------- -126: [02:22:54] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule -126: [02:22:54] done -126: [02:22:54] ------------------------------------- -126: [02:22:54] Test multithreading with the pattern FP +115: [23:09:49] test on : 365 molecules done +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +124: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +124: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +124: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +124: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +124: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +124: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +124: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +124: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +124: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +124: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +124: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +124: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: ..[23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +124: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +124: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +124: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +124: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +124: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +124: .[23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +124: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +124: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: ..[23:09:49] +124: +124: **** +124: Pre-condition Violation +124: Number of atom props not equal to number of atoms +124: Violation occurred on line 89 in file ./Code/GraphMol/Descriptors/BCUT.cpp +124: Failed Expression: atom_props.size() == num_atoms +124: ---------- +124: Stacktrace: +124: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +124: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +124: 2# RDKit::Descriptors::BCUT2D(RDKit::ROMol const&, std::vector > const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitDescriptors.so.1 +124: 3# 0x0000FFFF9B99C01C in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdMolDescriptors.so +124: 4# 0x0000FFFF9B9AF890 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdMolDescriptors.so +124: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +124: 6# 0x0000FFFFA01A15C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +124: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +124: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so +124: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so +124: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +124: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +124: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so +124: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +124: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +124: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +124: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +124: 17# 0x0000FFFF9DC64180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +124: 18# 0x0000FFFF9DC64118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +124: 19# 0x0000FFFF9DC640A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +124: 20# 0x0000FFFF9DC64040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +124: 21# 0x0000FFFF9DC63FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +124: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so +124: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so +124: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so +124: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so +124: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +124: 27# 0x0000FFFFA019E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +124: 28# _PyObject_MakeTpCall in /usr/bin/python3 +124: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 +124: 30# 0x00000000004C3D1C in /usr/bin/python3 +124: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 +124: 32# _PyObject_Call_Prepend in /usr/bin/python3 +124: 33# 0x000000000052608C in /usr/bin/python3 +124: 34# _PyObject_MakeTpCall in /usr/bin/python3 +124: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 +124: 36# 0x00000000004C3D1C in /usr/bin/python3 +124: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 +124: 38# _PyObject_Call_Prepend in /usr/bin/python3 +124: 39# 0x000000000052608C in /usr/bin/python3 +124: 40# _PyObject_MakeTpCall in /usr/bin/python3 +124: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 +124: 42# 0x00000000004C3D1C in /usr/bin/python3 +124: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 +124: 44# _PyObject_Call_Prepend in /usr/bin/python3 +124: 45# 0x000000000052608C in /usr/bin/python3 +124: 46# _PyObject_MakeTpCall in /usr/bin/python3 +124: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 +124: 48# _PyObject_Call_Prepend in /usr/bin/python3 +124: 49# 0x000000000051FB4C in /usr/bin/python3 +124: 50# 0x000000000051B324 in /usr/bin/python3 +124: 51# _PyObject_MakeTpCall in /usr/bin/python3 +124: 52# _PyEval_EvalFrameDefault in /usr/bin/python3 +124: 53# PyEval_EvalCode in /usr/bin/python3 +124: 54# 0x0000000000595200 in /usr/bin/python3 +124: 55# 0x00000000006757AC in /usr/bin/python3 +124: 56# _PyRun_SimpleFileObject in /usr/bin/python3 +124: 57# _PyRun_AnyFileObject in /usr/bin/python3 +124: 58# Py_RunMain in /usr/bin/python3 +124: 59# Py_BytesMain in /usr/bin/python3 +124: 60# 0x0000FFFFA09A229C in /lib/aarch64-linux-gnu/libc.so.6 +124: 61# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +124: 62# _start in /usr/bin/python3 +124: ---------- +124: **** +124: +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: ...Warning: Atom Count for residue GLU5A does not match expected count +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: Warning: Atom Count for residue ASN39A does not match expected count +124: Warning: Atom Count for residue GLU53A does not match expected count +124: Warning: Atom Count for residue ARG64A does not match expected count +124: Warning: Atom Count for residue LYS80A does not match expected count +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: Warning: Atom Count for residue GLU150A does not match expected count +124: Warning: Atom Count for residue ASN157A does not match expected count +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +123: Warning: Atom Count for residue GLU53A does not match expected count +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] done +126: [23:09:49] ------------------------------------- +126: [23:09:49] Test Hashed Atom Pairs. +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] done +126: [23:09:49] ------------------------------------- +126: [23:09:49] Test Hashed torsions. +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] done +126: [23:09:49] ------------------------------------- +126: [23:09:49] Test Rooted Atom Pairs. +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] done +126: [23:09:49] ------------------------------------- +126: [23:09:49] Test ignoring atoms in Atom Pairs. +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] done +126: [23:09:49] ------------------------------------- +126: [23:09:49] Test Rooted Topological Torsions. +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] done +126: [23:09:49] ------------------------------------- +126: [23:09:49] Test ignoring atoms in Topological Torsions. +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] done +126: [23:09:49] ------------------------------------- +126: [23:09:49] Test atom info from morgan fingerprints. +126: [23:09:49] done +126: [23:09:49] ------------------------------------- +126: [23:09:49] Test atom info from morgan fingerprints including Info Redundant Environments. +126: [23:09:49] done +126: [23:09:49] ------------------------------------- +126: [23:09:49] ------------------------------------- +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] ------------------------------------- +126: [23:09:49] ------------------------------------- +126: [23:09:49] ------------------------------------- +126: [23:09:49] ------------------------------------- +126: [23:09:49] Test Atom Pairs including info about chirality. +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] done +126: [23:09:49] ------------------------------------- +126: [23:09:49] Test Topological Torsions including info about chirality. +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] done +126: [23:09:49] ------------------------------------- +126: [23:09:49] Test GitHub Issue 25: fingerprint backwards compatibility. +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] done +126: [23:09:49] ------------------------------------- +126: [23:09:49] Test GitHub Issue 151: PatternFingerprint problems +126: [23:09:49] done +126: [23:09:49] ------------------------------------- +126: [23:09:49] Test 3D atom pairs. +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:49] done +126: [23:09:49] ------------------------------------- +126: [23:09:49] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule +126: [23:09:49] done +126: [23:09:49] ------------------------------------- +126: [23:09:49] Test multithreading with the pattern FP 126: reading molecules 126: pass 1 126: launch :0 126: launch :1 126: launch :2 126: launch :3 -123: Warning: Atom Count for residue GLU53A does not match expected count -115/230 Test #125: pyMolDescriptors3D ..................... Passed 0.80 sec +124: Warning: Atom Count for residue GLU5A does not match expected count +123: Warning: Atom Count for residue ARG64A does not match expected count +126: pass 2 +126: launch :0 +126: launch :1 +126: launch :2 +126: launch :3 +79: =============================================================================== +79: All tests passed (1586 assertions in 98 test cases) +79: +115/230 Test #79: fileParsersCatchTest ................... Passed 14.62 sec test 127 Start 127: testMHFPFingerprint 127: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/testMHFPFingerprint 127: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 127: Test timeout computed to be: 1500 -124: Warning: Atom Count for residue ASN39A does not match expected count -127: [02:22:54] ------------------------------------- -127: [02:22:54] Test MHFP fingerprint encoder initialization -127: [02:22:54] done -127: [02:22:54] ------------------------------------- -127: [02:22:54] Test MHFP shingling creation -127: [02:22:54] done -127: [02:22:54] ------------------------------------- -127: [02:22:54] Test MHFP hashing of string and uint arrays -127: [02:22:54] done -127: [02:22:54] ------------------------------------- -127: [02:22:54] Test SECFP fingerprint functionality -123: Warning: Atom Count for residue ARG64A does not match expected count -127: [02:22:54] done -116/230 Test #127: testMHFPFingerprint .................... Passed 0.09 sec +127: [23:09:50] ------------------------------------- +127: [23:09:50] Test MHFP fingerprint encoder initialization +127: [23:09:50] done +127: [23:09:50] ------------------------------------- +127: [23:09:50] Test MHFP shingling creation +127: [23:09:50] done +127: [23:09:50] ------------------------------------- +127: [23:09:50] Test MHFP hashing of string and uint arrays +127: [23:09:50] done +127: [23:09:50] ------------------------------------- +127: [23:09:50] Test SECFP fingerprint functionality +127: [23:09:50] done +116/230 Test #127: testMHFPFingerprint .................... Passed 0.18 sec test 128 Start 128: testFingerprintGenerators 128: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprintGenerators 128: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 128: Test timeout computed to be: 1500 -128: [02:22:54] ------------------------------------- -128: [02:22:54] Test atom-pair fp generator -126: pass 2 -126: launch :0 -126: launch :1 -126: launch :2 -126: launch :3 -128: [02:22:54] done -128: [02:22:54] ------------------------------------- -128: [02:22:54] Test atom-pair fp generator with different arguments -128: [02:22:54] done -128: [02:22:54] ------------------------------------- -128: [02:22:54] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation -128: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:22:54] DEPRECATION WARNING: please use AtomPairGenerator -128: [02:22:54] done -128: [02:22:54] ------------------------------------- -128: [02:22:54] Test atom-pair additional output -128: [02:22:54] done -128: [02:22:54] ------------------------------------- -128: [02:22:54] Test Folded Atom Pairs. -128: [02:22:54] done -128: [02:22:54] ------------------------------------- -128: [02:22:54] Test Rooted Atom Pairs. -128: [02:22:54] done -128: [02:22:54] ------------------------------------- -128: [02:22:54] Test ignoring atoms in Atom Pairs. -128: [02:22:54] done -128: [02:22:54] ------------------------------------- -128: [02:22:54] Test Atom Pairs including info about chirality. -128: [02:22:54] done -128: [02:22:54] ------------------------------------- -128: [02:22:54] Test Morgan Fingerprints. -128: [02:22:54] done -128: [02:22:54] ------------------------------------- -128: [02:22:54] Test morgan fp generator -124: Warning: Atom Count for residue GLU53A does not match expected count -128: [02:22:54] done -128: [02:22:54] ------------------------------------- -128: [02:22:54] Test Morgan Fingerprints using fromAtoms argument. -128: [02:22:54] done -128: [02:22:54] ------------------------------------- -128: [02:22:54] Test Morgan Fingerprints as bit vects. -128: [02:22:54] done -128: [02:22:54] ------------------------------------- -128: [02:22:54] Test Morgan Fingerprints with feature invariants. -128: [02:22:54] done -128: [02:22:54] ------------------------------------- -128: [02:22:54] Test additional Morgan fingerprints options. -128: [02:22:54] done -128: [02:22:54] ------------------------------------- -128: [02:22:54] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -128: [02:22:54] done -128: [02:22:54] ------------------------------------- -128: [02:22:54] Single atoms setting radius 1 bits in Morgan fingerprints -128: [02:22:54] done -128: [02:22:54] ------------------------------------- -128: [02:22:54] Test different invariant generator combinations -128: [02:22:54] done -128: [02:22:54] ------------------------------------- -128: [02:22:54] Test invariant overriding -128: [02:22:54] done -128: [02:22:54] ------------------------------------- -128: [02:22:54] Test RDKit fp generator -124: Warning: Atom Count for residue ARG64A does not match expected count 123: Warning: Atom Count for residue LYS80A does not match expected count -124: Warning: Atom Count for residue LYS80A does not match expected count -128: [02:22:55] done -128: [02:22:55] ------------------------------------- -128: [02:22:55] Test unfolded version of RDKFP -128: [02:22:55] ------------------------------------- -128: [02:22:55] Test topological torsion fp generator -128: [02:22:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:22:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:22:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:22:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:22:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:22:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:22:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:22:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:22:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:22:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [02:22:55] done -128: [02:22:55] ------------------------------------- -128: [02:22:55] Test Topological Torsions. -128: [02:22:55] done -128: [02:22:55] ------------------------------------- -128: [02:22:55] Test Folded torsions. -128: [02:22:55] done -128: [02:22:55] ------------------------------------- -128: [02:22:55] Test Bulk Topological Torsions. -128: [02:22:55] done -128: [02:22:55] ------------------------------------- -128: [02:22:55] Test Rooted Topological Torsions. -128: [02:22:55] done -128: [02:22:55] ------------------------------------- -128: [02:22:55] Test ignoring atoms in Topological Torsions. -128: [02:22:55] done -128: [02:22:55] ------------------------------------- -128: [02:22:55] ------------------------------------- -128: [02:22:55] Test Topological Torsions including info about chirality. -128: [02:22:55] done -128: [02:22:55] ------------------------------------- -128: [02:22:55] Test GitHub Issue 25: fingerprint backwards compatibility. -128: [02:22:55] done -128: [02:22:55] ------------------------------------- -128: [02:22:55] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -128: [02:22:55] done -128: [02:22:55] ------------------------------------- -128: [02:22:55] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -128: [02:22:55] done -128: [02:22:55] ------------------------------------- -128: [02:22:55] Test convenience and bulk fp calculation functions +128: [23:09:50] ------------------------------------- +128: [23:09:50] Test atom-pair fp generator +128: [23:09:50] done +128: [23:09:50] ------------------------------------- +128: [23:09:50] Test atom-pair fp generator with different arguments +128: [23:09:50] done +128: [23:09:50] ------------------------------------- +128: [23:09:50] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation +128: [23:09:50] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:09:50] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:09:50] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:09:50] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:09:50] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:09:50] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:09:50] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:09:50] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:09:50] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:09:50] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:09:50] done +128: [23:09:50] ------------------------------------- +128: [23:09:50] Test atom-pair additional output +128: [23:09:50] done +128: [23:09:50] ------------------------------------- +128: [23:09:50] Test Folded Atom Pairs. +128: [23:09:50] done +128: [23:09:50] ------------------------------------- +128: [23:09:50] Test Rooted Atom Pairs. +128: [23:09:50] done +128: [23:09:50] ------------------------------------- +128: [23:09:50] Test ignoring atoms in Atom Pairs. +128: [23:09:50] done +128: [23:09:50] ------------------------------------- +128: [23:09:50] Test Atom Pairs including info about chirality. +128: [23:09:50] done +128: [23:09:50] ------------------------------------- +128: [23:09:50] Test Morgan Fingerprints. +128: [23:09:50] done +128: [23:09:50] ------------------------------------- +128: [23:09:50] Test morgan fp generator +128: [23:09:50] done +128: [23:09:50] ------------------------------------- +128: [23:09:50] Test Morgan Fingerprints using fromAtoms argument. +128: [23:09:50] done +128: [23:09:50] ------------------------------------- +128: [23:09:50] Test Morgan Fingerprints as bit vects. +128: [23:09:50] done +128: [23:09:50] ------------------------------------- +128: [23:09:50] Test Morgan Fingerprints with feature invariants. +128: [23:09:50] done +128: [23:09:50] ------------------------------------- +128: [23:09:50] Test additional Morgan fingerprints options. +128: [23:09:50] done +128: [23:09:50] ------------------------------------- +128: [23:09:50] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +128: [23:09:50] done +128: [23:09:50] ------------------------------------- +128: [23:09:50] Single atoms setting radius 1 bits in Morgan fingerprints +128: [23:09:50] done +128: [23:09:50] ------------------------------------- +128: [23:09:50] Test different invariant generator combinations +128: [23:09:50] done +128: [23:09:50] ------------------------------------- +128: [23:09:50] Test invariant overriding +128: [23:09:50] done +128: [23:09:50] ------------------------------------- +128: [23:09:50] Test RDKit fp generator 120: =>start test GETAWAY -120: [02:22:55] test on : 365 molecules done -117/230 Test #120: testGETAWAY ............................ Passed 2.36 sec +120: [23:09:50] test on : 365 molecules done +117/230 Test #120: testGETAWAY ............................ Passed 3.49 sec test 129 Start 129: fpTestCatch 129: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/fpTestCatch 129: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 129: Test timeout computed to be: 1500 -129: Randomness seeded to: 272994961 +124: Warning: Atom Count for residue ASN39A does not match expected count +129: Randomness seeded to: 2374868848 129: =============================================================================== 129: All tests passed (188 assertions in 16 test cases) 129: -118/230 Test #129: fpTestCatch ............................ Passed 0.03 sec +118/230 Test #129: fpTestCatch ............................ Passed 0.11 sec test 130 Start 130: fpGenTestCatch 130: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/fpGenTestCatch 130: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 130: Test timeout computed to be: 1500 -130: Randomness seeded to: 1276602515 +130: Randomness seeded to: 1696528888 130: =============================================================================== 130: All tests passed (2692 assertions in 5 test cases) 130: -119/230 Test #130: fpGenTestCatch ......................... Passed 0.16 sec +119/230 Test #130: fpGenTestCatch ......................... Passed 0.24 sec test 131 Start 131: pyTestGenerator 131: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/Wrap/testGenerators.py" 131: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap 131: Test timeout computed to be: 1500 -93: 0,0 0 -93: 0,1 0 -93: 1,0 0 -93: 1,1 0 -93: 2,0 0 -93: 2,1 0 -120/230 Test #93: testEnumeration ........................ Passed 6.63 sec +124: Warning: Atom Count for residue GLU53A does not match expected count +124: Warning: Atom Count for residue ARG64A does not match expected count +128: [23:09:51] done +128: [23:09:51] ------------------------------------- +128: [23:09:51] Test unfolded version of RDKFP +128: [23:09:51] ------------------------------------- +128: [23:09:51] Test topological torsion fp generator +128: [23:09:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:09:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:09:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:09:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:09:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:09:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:09:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:09:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:09:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:09:51] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:09:51] done +128: [23:09:51] ------------------------------------- +128: [23:09:51] Test Topological Torsions. +128: [23:09:51] done +128: [23:09:51] ------------------------------------- +128: [23:09:51] Test Folded torsions. +128: [23:09:51] done +128: [23:09:51] ------------------------------------- +128: [23:09:51] Test Bulk Topological Torsions. +124: Warning: Atom Count for residue LYS80A does not match expected count +128: [23:09:51] done +128: [23:09:51] ------------------------------------- +128: [23:09:51] Test Rooted Topological Torsions. +128: [23:09:51] done +128: [23:09:51] ------------------------------------- +128: [23:09:51] Test ignoring atoms in Topological Torsions. +128: [23:09:51] done +128: [23:09:51] ------------------------------------- +128: [23:09:51] ------------------------------------- +128: [23:09:51] Test Topological Torsions including info about chirality. +128: [23:09:51] done +128: [23:09:51] ------------------------------------- +128: [23:09:51] Test GitHub Issue 25: fingerprint backwards compatibility. +128: [23:09:51] done +128: [23:09:51] ------------------------------------- +128: [23:09:51] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +128: [23:09:51] done +128: [23:09:51] ------------------------------------- +128: [23:09:51] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +128: [23:09:51] done +128: [23:09:51] ------------------------------------- +128: [23:09:51] Test convenience and bulk fp calculation functions +131: .............. +131: ---------------------------------------------------------------------- +131: Ran 14 tests in 0.246s +131: +131: OK +128: [23:09:52] done +128: [23:09:52] ------------------------------------- +128: [23:09:52] Test GitHub Issue #6958 +128: [23:09:52] DEPRECATION WARNING: please use AtomPairGenerator +120/230 Test #131: pyTestGenerator ........................ Passed 1.30 sec test 132 Start 132: pyTestMHFP 132: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Fingerprints/Wrap/testMHFP.py" 132: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap 132: Test timeout computed to be: 1500 -124: Warning: Atom Count for residue GLU150A does not match expected count -124: Warning: Atom Count for residue ASN157A does not match expected count -128: [02:22:56] done -128: [02:22:56] ------------------------------------- -128: [02:22:56] Test GitHub Issue #6958 -128: [02:22:56] DEPRECATION WARNING: please use AtomPairGenerator -121/230 Test #128: testFingerprintGenerators .............. Passed 1.34 sec +123: Warning: Atom Count for residue GLU150A does not match expected count +121/230 Test #128: testFingerprintGenerators .............. Passed 1.83 sec test 133 Start 133: testPartialCharges 133: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/testPartialCharges 133: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges 133: Test timeout computed to be: 1500 -123: Warning: Atom Count for residue GLU150A does not match expected count -122/230 Test #133: testPartialCharges ..................... Passed 0.04 sec +122/230 Test #133: testPartialCharges ..................... Passed 0.06 sec test 134 Start 134: pyPartialCharges @@ -26981,37 +27003,15 @@ 134: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/Wrap 134: Test timeout computed to be: 1500 123: Warning: Atom Count for residue ASN157A does not match expected count -132: .. -132: ---------------------------------------------------------------------- -132: Ran 2 tests in 0.039s -132: -132: OK -131: .............. -131: ---------------------------------------------------------------------- -131: Ran 14 tests in 0.301s -131: -131: OK -79: =============================================================================== -79: All tests passed (1586 assertions in 98 test cases) -79: -123/230 Test #79: fileParsersCatchTest ................... Passed 8.30 sec +115: =>start test GETAWAY custom +115: [23:09:52] test on : 365 molecules done +123/230 Test #115: testRDFcustom .......................... Passed 7.48 sec test 135 Start 135: testMolTransforms 135: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/testMolTransforms 135: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms 135: Test timeout computed to be: 1500 -124/230 Test #132: pyTestMHFP ............................. Passed 0.60 sec -test 136 - Start 136: molTransformsTestCatch - -136: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/molTransformsTestCatch -136: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms -136: Test timeout computed to be: 1500 -136: Randomness seeded to: 2750507485 -136: =============================================================================== -136: All tests passed (4 assertions in 1 test case) -136: 135: *********************************************************** 135: Testing MolTransforms 135: --------------------------------- @@ -27042,53 +27042,97 @@ 135: testWeightedCentroid 135: 135: *********************************************************** -125/230 Test #135: testMolTransforms ...................... Passed 0.05 sec +124/230 Test #135: testMolTransforms ...................... Passed 0.06 sec +test 136 + Start 136: molTransformsTestCatch + +136: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/molTransformsTestCatch +136: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms +136: Test timeout computed to be: 1500 +124: Warning: Atom Count for residue GLU150A does not match expected count +136: Randomness seeded to: 2186788052 +136: =============================================================================== +136: All tests passed (4 assertions in 1 test case) +136: +125/230 Test #136: molTransformsTestCatch ................. Passed 0.10 sec test 137 Start 137: pyMolTransforms 137: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolTransforms/Wrap/testMolTransforms.py" 137: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/Wrap 137: Test timeout computed to be: 1500 -126/230 Test #131: pyTestGenerator ........................ Passed 0.92 sec -127/230 Test #136: molTransformsTestCatch ................. Passed 0.06 sec +124: Warning: Atom Count for residue ASN157A does not match expected count +132: .. +132: ---------------------------------------------------------------------- +132: Ran 2 tests in 0.091s +132: +132: OK +134: ....... +134: ---------------------------------------------------------------------- +134: Ran 7 tests in 0.206s +134: +134: OK +126/230 Test #132: pyTestMHFP ............................. Passed 1.30 sec test 138 Start 138: forceFieldHelpersCatch 138: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/forceFieldHelpersCatch 138: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers 138: Test timeout computed to be: 1500 +138: Randomness seeded to: 261104481 +138: =============================================================================== +138: All tests passed (11 assertions in 1 test case) +138: +127/230 Test #138: forceFieldHelpersCatch ................. Passed 0.06 sec test 139 Start 139: testMMFFForceFieldHelpers 139: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpers 139: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 139: Test timeout computed to be: 1500 -138: Randomness seeded to: 3188146624 -138: =============================================================================== -138: All tests passed (11 assertions in 1 test case) -138: -128/230 Test #138: forceFieldHelpersCatch ................. Passed 0.04 sec +137: ........ +137: ---------------------------------------------------------------------- +137: Ran 8 tests in 0.064s +137: +137: OK +139: [23:09:53] ------------------------------------- +139: [23:09:53] Test MMFF atom types. +139: [23:09:53] done +139: [23:09:53] ------------------------------------- +139: [23:09:53] Testing MMFF builder tools. +139: [23:09:53] done +139: [23:09:53] ------------------------------------- +139: [23:09:53] Testing MMFF builder+minimization. +128/230 Test #134: pyPartialCharges ....................... Passed 1.43 sec test 140 Start 140: testMMFFForceFieldHelpersMultiThread 140: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpersMultiThread 140: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 140: Test timeout computed to be: 1500 -139: [02:22:56] ------------------------------------- -139: [02:22:56] Test MMFF atom types. -140: [02:22:56] ------------------------------------- -140: [02:22:56] Test MMFF multithreading -139: [02:22:56] done -139: [02:22:56] ------------------------------------- -139: [02:22:56] Testing MMFF builder tools. -139: [02:22:56] done -139: [02:22:56] ------------------------------------- -139: [02:22:56] Testing MMFF builder+minimization. -134: ....... -134: ---------------------------------------------------------------------- -134: Ran 7 tests in 0.105s -134: -134: OK +129/230 Test #137: pyMolTransforms ........................ Passed 0.77 sec +test 141 + Start 141: testUFFForceFieldHelpers + +141: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers +141: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF +141: Test timeout computed to be: 1500 +140: [23:09:53] ------------------------------------- +140: [23:09:53] Test MMFF multithreading +141: [23:09:53] ------------------------------------- +141: [23:09:53] Test UFF atom labels. +141: [23:09:53] done +141: [23:09:53] ------------------------------------- +141: [23:09:53] Test UFF atom typer. +141: [23:09:53] done +141: [23:09:53] ------------------------------------- +141: [23:09:53] Testing UFF builder tools. +141: [23:09:53] done +141: [23:09:53] ------------------------------------- +141: [23:09:53] Testing UFF builder+minimization. +139: [23:09:53] done +139: [23:09:53] ------------------------------------- +139: [23:09:53] Testing Issue239. 140: processing 140: launch :0 140: launch :1 @@ -27114,585 +27158,952 @@ 140: launch :21 140: launch :22 140: launch :23 -139: [02:22:56] done -139: [02:22:56] ------------------------------------- -139: [02:22:56] Testing Issue239. -139: [02:22:56] done -139: [02:22:56] ------------------------------------- -139: [02:22:56] Testing calcEnergy with passed coords. -139: [02:22:56] done -139: [02:22:56] ------------------------------------- -139: [02:22:56] Testing calcGrad. -139: [02:22:56] done -139: [02:22:56] ------------------------------------- -139: [02:22:56] Testing Issue242. -129/230 Test #134: pyPartialCharges ....................... Passed 0.71 sec -test 141 - Start 141: testUFFForceFieldHelpers - -141: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers -141: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF -141: Test timeout computed to be: 1500 -139: [02:22:57] done -139: [02:22:57] ------------------------------------- -139: [02:22:57] Testing github 308: crash during MMFF parameterization . -139: [02:22:57] ------------------------------------- -139: [02:22:57] Testing SFIssue1653802. -139: [02:22:57] done -139: [02:22:57] ------------------------------------- -139: [02:22:57] Testing SFIssue2378119. -139: [02:22:57] done -139: [02:22:57] ------------------------------------- -139: [02:22:57] Test MMFF force-field parameter getters. -139: [02:22:57] ------------------------------------- -139: [02:22:57] Test MMFF multithreading -141: [02:22:57] ------------------------------------- -141: [02:22:57] Test UFF atom labels. +139: [23:09:53] done +139: [23:09:53] ------------------------------------- +139: [23:09:53] Testing calcEnergy with passed coords. +139: [23:09:53] done +139: [23:09:53] ------------------------------------- +139: [23:09:53] Testing calcGrad. +141: [23:09:53] done +141: [23:09:53] ------------------------------------- +141: [23:09:53] Testing UFF special cases. +141: [23:09:53] UFFTYPER: Unrecognized charge state for atom: 0 +141: [23:09:53] done +141: [23:09:53] ------------------------------------- +141: [23:09:53] Testing Issue239. +141: [23:09:53] done +141: [23:09:53] ------------------------------------- +141: [23:09:53] Testing calcEnergy with passed coords. +141: [23:09:53] done +141: [23:09:53] ------------------------------------- +141: [23:09:53] Testing calcGrad. +141: [23:09:53] done +141: [23:09:53] ------------------------------------- +141: [23:09:53] Testing SFIssue1653802. +141: [23:09:53] done +141: [23:09:53] ------------------------------------- +141: [23:09:53] Testing SFIssue2378119. +139: [23:09:53] done +139: [23:09:53] ------------------------------------- +139: [23:09:53] Testing Issue242. +141: [23:09:53] done +141: [23:09:53] ------------------------------------- +141: [23:09:53] Test UFF force-field parameter getters. +141: [23:09:53] ------------------------------------- +141: [23:09:53] Testing handling missing parameters. +141: [23:09:53] UFFTYPER: Unrecognized hybridization for atom: 0 +141: [23:09:53] UFFTYPER: Unrecognized atom type: Cu+1 (0) +141: [23:09:53] UFFTYPER: Unrecognized hybridization for atom: 0 +141: [23:09:53] UFFTYPER: Unrecognized atom type: Cu+1 (0) +141: [23:09:53] done +141: [23:09:53] ------------------------------------- +141: [23:09:53] Testing SFIssue3009337. +141: [23:09:53] done +141: [23:09:53] ------------------------------------- +141: [23:09:53] Test UFF multithreading +141: generating reference data +139: [23:09:53] done +139: [23:09:53] ------------------------------------- +139: [23:09:53] Testing github 308: crash during MMFF parameterization . +139: [23:09:53] ------------------------------------- +139: [23:09:53] Testing SFIssue1653802. +139: [23:09:53] done +139: [23:09:53] ------------------------------------- +139: [23:09:53] Testing SFIssue2378119. +139: [23:09:53] done +139: [23:09:53] ------------------------------------- +139: [23:09:53] Test MMFF force-field parameter getters. +139: [23:09:53] ------------------------------------- +139: [23:09:53] Test MMFF multithreading 139: generating reference data -141: [02:22:57] done -141: [02:22:57] ------------------------------------- -141: [02:22:57] Test UFF atom typer. -141: [02:22:57] done -141: [02:22:57] ------------------------------------- -141: [02:22:57] Testing UFF builder tools. -141: [02:22:57] done -141: [02:22:57] ------------------------------------- -141: [02:22:57] Testing UFF builder+minimization. -27: Checking against /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -141: [02:22:57] done -141: [02:22:57] ------------------------------------- -141: [02:22:57] Testing UFF special cases. -141: [02:22:57] UFFTYPER: Unrecognized charge state for atom: 0 -141: [02:22:57] done -141: [02:22:57] ------------------------------------- -141: [02:22:57] Testing Issue239. -141: [02:22:57] done -141: [02:22:57] ------------------------------------- -141: [02:22:57] Testing calcEnergy with passed coords. -141: [02:22:57] done -141: [02:22:57] ------------------------------------- -141: [02:22:57] Testing calcGrad. -137: ........ -137: ---------------------------------------------------------------------- -137: Ran 8 tests in 0.204s -137: -137: OK -141: [02:22:57] done -141: [02:22:57] ------------------------------------- -141: [02:22:57] Testing SFIssue1653802. -141: [02:22:57] done -141: [02:22:57] ------------------------------------- -141: [02:22:57] Testing SFIssue2378119. -141: [02:22:57] done -141: [02:22:57] ------------------------------------- -141: [02:22:57] Test UFF force-field parameter getters. -141: [02:22:57] ------------------------------------- -141: [02:22:57] Testing handling missing parameters. -141: [02:22:57] UFFTYPER: Unrecognized hybridization for atom: 0 -141: [02:22:57] UFFTYPER: Unrecognized atom type: Cu+1 (0) -141: [02:22:57] UFFTYPER: Unrecognized hybridization for atom: 0 -141: [02:22:57] UFFTYPER: Unrecognized atom type: Cu+1 (0) 140: done -141: [02:22:57] done -141: [02:22:57] ------------------------------------- -141: [02:22:57] Testing SFIssue3009337. -141: [02:22:57] done -141: [02:22:57] ------------------------------------- -141: [02:22:57] Test UFF multithreading -140: [02:22:57] done -27: All 191 tests passed -141: generating reference data -115: =>start test GETAWAY custom -115: [02:22:57] test on : 365 molecules done -130/230 Test #115: testRDFcustom .......................... Passed 5.28 sec +140: [23:09:54] done +130/230 Test #140: testMMFFForceFieldHelpersMultiThread ... Passed 0.64 sec test 142 Start 142: testCrystalForceField 142: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalForceField 142: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF 142: Test timeout computed to be: 1500 -131/230 Test #140: testMMFFForceFieldHelpersMultiThread ... Passed 0.64 sec +142: ------------------------------------- +142: Test CrystalFF torsional term. +141: processing +141: launch :0 +141: launch :1 +141: launch :2 +141: launch :3 +141: [23:09:54] Rep: [23:09:54] Rep: 0 Mol:3 +141: 0 Mol:2 +141: [23:09:54] Rep: 0 Mol:1 +141: [23:09:54] Rep: 0 Mol:0 +141: [23:09:54] Rep: 0 Mol:5 +141: [23:09:54] Rep: 0 Mol:9 +141: [23:09:54] Rep: 0 Mol:4 +141: [23:09:54] Rep: 0 Mol:13 +141: [23:09:54] Rep: 0 Mol:7 +141: [23:09:54] Rep: 0 Mol:11 +141: [23:09:54] Rep: 0 Mol:15 +141: [23:09:54] Rep: 0 Mol:6 +141: [23:09:54] Rep: 0 Mol:10 +141: [23:09:54] Rep: 0 Mol:17 +141: [23:09:54] Rep: 0 Mol:19 +141: [23:09:54] Rep: 0 Mol:23 +141: [23:09:54] Rep: 0 Mol:27 +141: [23:09:54] Rep: 0 Mol:31 +141: [23:09:54] Rep: 0 Mol:8 +141: [23:09:54] Rep: 0 Mol:14 +141: [23:09:54] Rep: 0 Mol:12 +141: [23:09:54] Rep: 0 Mol:16 +141: [23:09:54] Rep: 0 Mol:18 +141: [23:09:54] Rep: 0 Mol:21 +141: [23:09:54] Rep: 0 Mol:25 +141: [23:09:54] Rep: 0 Mol:20 +141: [23:09:54] Rep: 0 Mol:22 +141: [23:09:54] Rep: 0 Mol:26 +141: [23:09:54] Rep: 0 Mol:29 +141: [23:09:54] Rep: 0 Mol:24 +141: [23:09:54] Rep: 0 Mol:30 +141: [23:09:54] Rep: 0 Mol:28 +131/230 Test #142: testCrystalForceField .................. Passed 0.23 sec test 143 Start 143: pyForceFieldHelpers 143: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ForceFieldHelpers/Wrap/testHelpers.py" 143: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap 143: Test timeout computed to be: 1500 -142: ------------------------------------- -142: Test CrystalFF torsional term. -132/230 Test #137: pyMolTransforms ........................ Passed 0.72 sec +139: processing +139: launch :0 +139: launch :1 +139: launch :2 +139: launch :3 +139: [23:09:54] Rep: 0 Mol:0 +139: [23:09:54] Rep: 0 Mol:1 +139: [23:09:54] Rep: 0 Mol:5 +139: [23:09:54] Rep: 0 Mol:4 +139: [23:09:54] Rep: 0 Mol:2 +139: [23:09:54] Rep: 0 Mol:3 +139: [23:09:54] Rep: 0 Mol:9 +139: [23:09:54] Rep: 0 Mol:13 +139: [23:09:54] Rep: 0 Mol:17 +139: [23:09:54] Rep: 0 Mol:8 +139: [23:09:54] Rep: 0 Mol:12 +139: [23:09:54] Rep: 0 Mol:16 +139: [23:09:54] Rep: 0 Mol:6 +139: [23:09:54] Rep: 0 Mol:10 +139: [23:09:54] Rep: 0 Mol:20 +139: [23:09:54] Rep: 0 Mol:24 +139: [23:09:54] Rep: 0 Mol:21 +139: [23:09:54] Rep: 0 Mol:28 +139: [23:09:54] Rep: 0 Mol:7 +139: [23:09:54] Rep: 0 Mol:11 +139: [23:09:54] Rep: 0 Mol:25 +139: [23:09:54] Rep: 0 Mol:29 +139: [23:09:54] Rep: 0 Mol:15 +139: [23:09:54] Rep: 0 Mol:19 +139: [23:09:54] Rep: 0 Mol:23 +139: [23:09:54] Rep: 0 Mol:27 +139: [23:09:54] Rep: 0 Mol:31 +141: [23:09:54] Rep: 100 Mol:3 +141: [23:09:54] Rep: 100 Mol:7 +141: [23:09:54] Rep: 100 Mol:11 +141: [23:09:54] Rep: 100 Mol:15 +141: [23:09:54] Rep: 100 Mol:19 +141: [23:09:55] Rep: 100 Mol:23 +141: [23:09:55] Rep: 100 Mol:27 +141: [23:09:55] Rep: 100 Mol:31 +139: [23:09:55] Rep: 0 Mol:14 +139: [23:09:55] Rep: 0 Mol:18 +143: [23:09:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [23:09:55] Molecule does not have explicit Hs. Consider calling AddHs() +143: [23:09:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [23:09:55] Molecule does not have explicit Hs. Consider calling AddHs() +143: [23:09:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [23:09:55] Molecule does not have explicit Hs. Consider calling AddHs() +143: [23:09:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [23:09:55] Molecule does not have explicit Hs. Consider calling AddHs() +143: [23:09:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [23:09:55] Molecule does not have explicit Hs. Consider calling AddHs() +143: ..[23:09:55] Molecule does not have explicit Hs. Consider calling AddHs() +143: [23:09:55] Molecule does not have explicit Hs. Consider calling AddHs() +143: .[23:09:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [23:09:55] Molecule does not have explicit Hs. Consider calling AddHs() +143: .[23:09:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [23:09:55] Molecule does not have explicit Hs. Consider calling AddHs() +139: [23:09:55] Rep: 0 Mol:22 +139: [23:09:55] Rep: 0 Mol:26 +139: [23:09:55] Rep: 0 Mol:30 +143: .[23:09:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [23:09:55] Molecule does not have explicit Hs. Consider calling AddHs() +143: .[23:09:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [23:09:55] Molecule does not have explicit Hs. Consider calling AddHs() +139: [23:09:55] Rep: 20 Mol:0 +139: [23:09:55] Rep: 20 Mol:4 +139: [23:09:55] Rep: 20 Mol:8 +139: [23:09:55] Rep: 20 Mol:12 +139: [23:09:55] Rep: 20 Mol:16 +139: [23:09:55] Rep: 20 Mol:20 +143: .[23:09:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [23:09:55] Molecule does not have explicit Hs. Consider calling AddHs() +143: .[23:09:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [23:09:55] Molecule does not have explicit Hs. Consider calling AddHs() +143: .[23:09:55] UFFTYPER: Unrecognized hybridization for atom: 0 +143: [23:09:55] UFFTYPER: Unrecognized atom type: Cu+1 (0) +143: .[23:09:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [23:09:55] Molecule does not have explicit Hs. Consider calling AddHs() +143: [23:09:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [23:09:55] Molecule does not have explicit Hs. Consider calling AddHs() +143: [23:09:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [23:09:55] Molecule does not have explicit Hs. Consider calling AddHs() +143: [23:09:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [23:09:55] Molecule does not have explicit Hs. Consider calling AddHs() +143: [23:09:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [23:09:55] Molecule does not have explicit Hs. Consider calling AddHs() +143: .[23:09:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [23:09:55] Molecule does not have explicit Hs. Consider calling AddHs() +139: [23:09:55] Rep: 20 Mol:24 +139: [23:09:55] Rep: 20 Mol:28 +143: .[23:09:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [23:09:55] Molecule does not have explicit Hs. Consider calling AddHs() +143: .[23:09:55] Molecule does not have explicit Hs. Consider calling AddHs() +143: [23:09:55] Molecule does not have explicit Hs. Consider calling AddHs() +143: ...[23:09:55] Molecule does not have explicit Hs. Consider calling AddHs() +143: [23:09:55] Molecule does not have explicit Hs. Consider calling AddHs() +143: [23:09:55] Molecule does not have explicit Hs. Consider calling AddHs() +141: [23:09:55] Rep: 100 Mol:2 +141: [23:09:55] Rep: 100 Mol:6 +139: [23:09:55] Rep: 20 Mol:1 +139: [23:09:55] Rep: 20 Mol:5 +139: [23:09:55] Rep: 20 Mol:9 +139: [23:09:55] Rep: 20 Mol:13 +139: [23:09:55] Rep: 20 Mol:17 +139: [23:09:55] Rep: 20 Mol:21 +139: [23:09:55] Rep: 20 Mol:25 +139: [23:09:55] Rep: 20 Mol:29 +141: [23:09:55] Rep: 100 Mol:10 +141: [23:09:55] Rep: 100 Mol:14 +141: [23:09:55] Rep: 100 Mol:18 +141: [23:09:55] Rep: 100 Mol:22 +141: [23:09:55] Rep: 100 Mol:26 +141: [23:09:55] Rep: 100 Mol:30 +139: [23:09:55] Rep: 20 Mol:3 +139: [23:09:55] Rep: 20 Mol:7 +139: [23:09:55] Rep: 20 Mol:11 +139: [23:09:55] Rep: 20 Mol:15 +139: [23:09:55] Rep: 20 Mol:19 +139: [23:09:55] Rep: 20 Mol:23 +139: [23:09:55] Rep: 20 Mol:27 +139: [23:09:55] Rep: 20 Mol:31 +143: ... +143: ---------------------------------------------------------------------- +143: Ran 19 tests in 0.287s +143: +143: OK +141: [23:09:55] Rep: 100 Mol:0 +141: [23:09:55] Rep: 100 Mol:4 +141: [23:09:55] Rep: 100 Mol:8 +141: [23:09:55] Rep: 100 Mol:12 +141: [23:09:55] Rep: 100 Mol:16 +141: [23:09:55] Rep: 100 Mol:20 +141: [23:09:55] Rep: 100 Mol:24 +141: [23:09:55] Rep: 100 Mol:28 +141: [23:09:55] Rep: 100 Mol:1 +141: [23:09:55] Rep: 100 Mol:5 +141: [23:09:55] Rep: 100 Mol:9 +141: [23:09:55] Rep: 100 Mol:13 +141: [23:09:55] Rep: 100 Mol:17 +141: [23:09:55] Rep: 100 Mol:21 +141: [23:09:55] Rep: 100 Mol:25 +141: [23:09:55] Rep: 100 Mol:29 +132/230 Test #143: pyForceFieldHelpers .................... Passed 1.17 sec test 144 Start 144: testDistGeomHelpers 144: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/testDistGeomHelpers 144: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers 144: Test timeout computed to be: 1500 -27: -27: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... -144: [02:22:57] ******************************************************** -144: [02:22:57] Testing DistGeomHelpers -144: [02:22:57] --------------------------------- -144: [02:22:57] test2 +139: [23:09:55] Rep: 40 Mol:0 +139: [23:09:55] Rep: 40 Mol:4 +139: [23:09:55] Rep: 40 Mol:8 +139: [23:09:55] Rep: 40 Mol:12 +139: [23:09:55] Rep: 40 Mol:16 +139: [23:09:55] Rep: 40 Mol:20 +139: [23:09:55] Rep: 40 Mol:24 +139: [23:09:55] Rep: 40 Mol:28 +139: [23:09:55] Rep: 40 Mol:3 +139: [23:09:55] Rep: 40 Mol:7 +139: [23:09:55] Rep: 40 Mol:11 +139: [23:09:55] Rep: 40 Mol:15 +139: [23:09:55] Rep: 40 Mol:19 +139: [23:09:55] Rep: 40 Mol:23 +139: [23:09:55] Rep: 40 Mol:27 +139: [23:09:55] Rep: 40 Mol:31 +144: [23:09:55] ******************************************************** +144: [23:09:55] Testing DistGeomHelpers +144: [23:09:55] --------------------------------- +144: [23:09:55] test2 144: 144: go 144: ------------------------------------- 144: -139: processing -139: launch :0 -139: launch :1 -139: launch :2 -139: launch :3 -139: [02:22:57] Rep: 0 Mol:1 -139: [02:22:57] Rep: 0 Mol:5 -139: [02:22:57] Rep: 0 Mol:2 -139: [02:22:57] Rep: 0 Mol:0 -139: [02:22:57] Rep: 0 Mol:3 -139: [02:22:57] Rep: 0 Mol:9 -139: [02:22:57] Rep: 0 Mol:13 -139: [02:22:57] Rep: 0 Mol:17 -133/230 Test #142: testCrystalForceField .................. Passed 0.20 sec +139: [23:09:55] Rep: 40 Mol:1 +139: [23:09:55] Rep: 40 Mol:5 +139: [23:09:55] Rep: 40 Mol:9 +139: [23:09:55] Rep: 40 Mol:13 +139: [23:09:55] Rep: 40 Mol:17 +139: [23:09:55] Rep: 40 Mol:21 +139: [23:09:55] Rep: 40 Mol:25 +139: [23:09:55] Rep: 40 Mol:29 +139: [23:09:55] Rep: 20 Mol:2 +139: [23:09:55] Rep: 20 Mol:6 +139: [23:09:55] Rep: 20 Mol:10 +139: [23:09:55] Rep: 20 Mol:14 +139: [23:09:55] Rep: 20 Mol:18 +139: [23:09:55] Rep: 20 Mol:22 +139: [23:09:55] Rep: 20 Mol:26 +139: [23:09:55] Rep: 20 Mol:30 +139: [23:09:55] Rep: 60 Mol:3 +139: [23:09:55] Rep: 60 Mol:7 +139: [23:09:55] Rep: 60 Mol:11 +139: [23:09:55] Rep: 60 Mol:15 +139: [23:09:55] Rep: 60 Mol:19 +139: [23:09:55] Rep: 60 Mol:23 +139: [23:09:55] Rep: 60 Mol:27 +139: [23:09:55] Rep: 60 Mol:31 +139: [23:09:55] Rep: 60 Mol:0 +139: [23:09:55] Rep: 60 Mol:4 +139: [23:09:55] Rep: 60 Mol:8 +139: [23:09:55] Rep: 60 Mol:12 +139: [23:09:55] Rep: 60 Mol:16 +139: [23:09:55] Rep: 60 Mol:20 +139: [23:09:55] Rep: 60 Mol:24 +139: [23:09:55] Rep: 60 Mol:28 +139: [23:09:56] Rep: 60 Mol:1 +139: [23:09:56] Rep: 60 Mol:5 +139: [23:09:56] Rep: 60 Mol:9 +139: [23:09:56] Rep: 60 Mol:13 +139: [23:09:56] Rep: 60 Mol:17 +139: [23:09:56] Rep: 60 Mol:21 +139: [23:09:56] Rep: 60 Mol:25 +139: [23:09:56] Rep: 60 Mol:29 +139: [23:09:56] Rep: 80 Mol:3 +139: [23:09:56] Rep: 80 Mol:7 +139: [23:09:56] Rep: 80 Mol:11 +139: [23:09:56] Rep: 80 Mol:15 +139: [23:09:56] Rep: 80 Mol:19 +139: [23:09:56] Rep: 80 Mol:23 +139: [23:09:56] Rep: 80 Mol:27 +139: [23:09:56] Rep: 80 Mol:31 +139: [23:09:56] Rep: 80 Mol:0 +139: [23:09:56] Rep: 80 Mol:4 +139: [23:09:56] Rep: 80 Mol:8 +139: [23:09:56] Rep: 80 Mol:12 +139: [23:09:56] Rep: 80 Mol:16 +139: [23:09:56] Rep: 80 Mol:20 +139: [23:09:56] Rep: 80 Mol:24 +139: [23:09:56] Rep: 80 Mol:28 +139: [23:09:56] Rep: 40 Mol:2 +139: [23:09:56] Rep: 40 Mol:6 +139: [23:09:56] Rep: 40 Mol:10 +139: [23:09:56] Rep: 40 Mol:14 +139: [23:09:56] Rep: 40 Mol:18 +139: [23:09:56] Rep: 40 Mol:22 +139: [23:09:56] Rep: 40 Mol:26 +139: [23:09:56] Rep: 40 Mol:30 +141: [23:09:56] done +141: [23:09:56] ------------------------------------- +141: [23:09:56] Test UFF multithreading2 +139: [23:09:56] Rep: 80 Mol:1 +139: [23:09:56] Rep: 80 Mol:5 +139: [23:09:56] Rep: 80 Mol:9 +139: [23:09:56] Rep: 80 Mol:13 +139: [23:09:56] Rep: 80 Mol:17 +139: [23:09:56] Rep: 80 Mol:21 +139: [23:09:56] Rep: 80 Mol:25 +139: [23:09:56] Rep: 80 Mol:29 +139: [23:09:56] Rep: 60 Mol:2 +139: [23:09:56] Rep: 60 Mol:6 +139: [23:09:56] Rep: 60 Mol:10 +139: [23:09:56] Rep: 60 Mol:14 +139: [23:09:56] Rep: 60 Mol:18 +139: [23:09:56] Rep: 60 Mol:22 +139: [23:09:56] Rep: 60 Mol:26 +139: [23:09:56] Rep: 60 Mol:30 +126: [23:09:57] done +126: [23:09:57] ------------------------------------- +126: [23:09:57] Test GitHub Issue 258: Bad pattern fingerprint for query molecule +126: [23:09:57] done +126: [23:09:57] ------------------------------------- +126: [23:09:57] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +126: [23:09:57] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:57] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:57] done +126: [23:09:57] ------------------------------------- +126: [23:09:57] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +126: [23:09:57] done +126: [23:09:57] ------------------------------------- +126: [23:09:57] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +126: [23:09:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:57] done +126: [23:09:57] ------------------------------------- +126: [23:09:57] Test unfolded version of RDKFP +126: [23:09:57] ------------------------------------- +126: [23:09:57] Test bitinfo of RDKFP +126: 562: [ 2 ], +126: 709: [ 0 1 ], +126: 1118: [ 0 1 2 ], +126: 1183: [ 1 2 ], +126: 1233: [ 0 1 2 ], +126: 1308: [ 0 ], [ 1 ], +126: 1339: [ 2 ], +126: 1728: [ 1 2 ], +126: 1772: [ 0 ], [ 1 ], +126: 1813: [ 0 1 ], +126: ------------ +126: [23:09:57] ------------------------------------- +126: [23:09:57] Single atoms setting radius 1 bits in Morgan fingerprints +126: [23:09:57] done +126: [23:09:57] ------------------------------------- +126: [23:09:57] Github #879: Pattern fingerprint should set bits for single-atom fragments. +126: [23:09:57] done +126: [23:09:57] ------------------------------------- +126: [23:09:57] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms +126: [23:09:57] done +126: [23:09:57] ------------------------------------- +126: [23:09:57] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False +126: [23:09:57] done +126: [23:09:57] ------------------------------------- +126: [23:09:57] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called +126: [23:09:57] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:57] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:57] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:57] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:57] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:57] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:57] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:57] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:57] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:57] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:57] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:57] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:09:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:09:57] done +126: [23:09:57] ------------------------------------- +126: [23:09:57] Github #2115: BitInfo not complete for RDKFingerprint +126: [23:09:57] done +126: [23:09:57] ------------------------------------- +126: [23:09:57] Github #3723: Fingerprint crash for mols with Zero order bonds +126: [23:09:57] done +133/230 Test #126: testFingerprints ....................... Passed 7.85 sec test 145 Start 145: distGeomHelpersCatch 145: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/distGeomHelpersCatch 145: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers 145: Test timeout computed to be: 1500 -139: [02:22:57] Rep: 0 Mol:4 -139: [02:22:57] Rep: 0 Mol:21 -139: [02:22:57] Rep: 0 Mol:25 -145: Randomness seeded to: 3063908466 -139: [02:22:57] Rep: 0 Mol:29 -139: [02:22:57] Rep: 0 Mol:6 -139: [02:22:57] Rep: 0 Mol:10 -139: [02:22:57] Rep: 0 Mol:8 -145: [02:22:57] [C:1][NH:2]!@;-[C:3](=[NH2:4])[NH2]: 100 101 102 104, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [NH2][C:1](=[NH2])[NH:2]!@;-[CH2:3][C:4]: 102 101 100 99, [(1 0), (1 0), (1 2.5), (1 0), (1 0), (1 0)] -139: [02:22:57] Rep: 0 Mol:12 -145: [02:22:57] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 32 31 30 33, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -145: [02:22:57] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 48 46 45 49, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -145: [02:22:57] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 36 37 38 39, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -145: [02:22:57] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 37 38 39 40, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -145: [02:22:57] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 38 39 40 41, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -145: [02:22:57] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 97 98 99 100, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -145: [02:22:57] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 98 99 100 101, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -145: [02:22:57] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 0 1 2 3, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -145: [02:22:57] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 1 2 4 5, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -145: [02:22:57] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 20 22 23 24, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -145: [02:22:57] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 22 23 25 26, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -145: [02:22:57] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 34 36 37 38, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -145: [02:22:57] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 66 67 68 69, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -145: [02:22:57] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 84 85 86 87, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -145: [02:22:57] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -145: [02:22:57] [C:1][CX4H2:2]!@;-[CX3:3]=[O:4]: 85 86 87 88, [(1 -1), (1 -0.5), (1 -0.2), (1 -0.3), (1 0), (1 -0.3)] -145: [02:22:57] [cH1:1][c:2]([cH1])!@;-[CX4H2:3][CX4:4]: 70 69 68 67, [(1 0), (1 3.6), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 15 13 12 8, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 22 20 19 15, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 67 75 77 81, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 4 62 61 60, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 8 6 5 4, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 30 28 27 22, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 36 34 33 30, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 45 43 42 36, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 81 82 84 85, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 93 94 96 97, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 97 105 107 52, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -139: [02:22:57] Rep: 0 Mol:7 -139: [02:22:57] Rep: 0 Mol:11 -145: [02:22:57] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 90 92 93 94, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -145: [02:22:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 6 5 4 117, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 28 27 22 133, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 34 33 30 144, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 43 42 36 149, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 62 61 60 181, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 82 84 85 202, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 94 96 97 210, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 105 107 52 171, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 91 90 92 93, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 43 45 49 50, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] -145: [02:22:57] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 52 50 49 45, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] -145: [02:22:57] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 60 64 66 67, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] -145: [02:22:57] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 68 67 66 64, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] -139: [02:22:57] Rep: 0 Mol:16 -145: [02:22:57] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 95 94 93 92, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 51 50 52 107, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -145: [02:22:57] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 65 64 60 61, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -145: [02:22:57] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 50 52 53 54, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -145: [02:22:57] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 58 59 60 61, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -145: [02:22:57] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 5 4 62 63, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 27 22 20 21, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 33 30 28 29, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 42 36 34 35, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 49 45 43 44, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 66 67 75 76, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 84 85 90 91, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 96 97 105 106, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +145: Randomness seeded to: 2905587312 +145: [23:09:57] [C:1][NH:2]!@;-[C:3](=[NH2:4])[NH2]: 100 101 102 104, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [NH2][C:1](=[NH2])[NH:2]!@;-[CH2:3][C:4]: 102 101 100 99, [(1 0), (1 0), (1 2.5), (1 0), (1 0), (1 0)] +141: [23:09:57] done +141: [23:09:57] ------------------------------------- +141: [23:09:57] Test UFF multithreading3 +145: [23:09:57] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 32 31 30 33, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +145: [23:09:57] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 48 46 45 49, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +145: [23:09:57] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 36 37 38 39, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +145: [23:09:57] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 37 38 39 40, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +145: [23:09:57] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 38 39 40 41, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +145: [23:09:57] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 97 98 99 100, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +145: [23:09:57] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 98 99 100 101, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +145: [23:09:57] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 0 1 2 3, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +145: [23:09:57] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 1 2 4 5, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +145: [23:09:57] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 20 22 23 24, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +145: [23:09:57] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 22 23 25 26, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +145: [23:09:57] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 34 36 37 38, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +145: [23:09:57] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 66 67 68 69, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +145: [23:09:57] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 84 85 86 87, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +145: [23:09:57] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +145: [23:09:57] [C:1][CX4H2:2]!@;-[CX3:3]=[O:4]: 85 86 87 88, [(1 -1), (1 -0.5), (1 -0.2), (1 -0.3), (1 0), (1 -0.3)] +145: [23:09:57] [cH1:1][c:2]([cH1])!@;-[CX4H2:3][CX4:4]: 70 69 68 67, [(1 0), (1 3.6), (1 0), (1 0), (1 0), (1 0)] +139: [23:09:57] Rep: 80 Mol:2 +139: [23:09:57] Rep: 80 Mol:6 +139: [23:09:57] Rep: 80 Mol:10 +145: [23:09:57] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 15 13 12 8, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 22 20 19 15, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 67 75 77 81, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 4 62 61 60, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 8 6 5 4, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 30 28 27 22, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 36 34 33 30, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 45 43 42 36, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 81 82 84 85, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 93 94 96 97, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 97 105 107 52, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 90 92 93 94, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +145: [23:09:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 6 5 4 117, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 28 27 22 133, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 34 33 30 144, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 43 42 36 149, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 62 61 60 181, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 82 84 85 202, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 94 96 97 210, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 105 107 52 171, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 91 90 92 93, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 43 45 49 50, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] +145: [23:09:57] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 52 50 49 45, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] +145: [23:09:57] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 60 64 66 67, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] +145: [23:09:57] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 68 67 66 64, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] +139: [23:09:57] Rep: 80 Mol:14 +139: [23:09:57] Rep: 80 Mol:18 +139: [23:09:57] Rep: 80 Mol:22 +139: [23:09:57] Rep: 80 Mol:26 +139: [23:09:57] Rep: 80 Mol:30 +145: [23:09:57] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 95 94 93 92, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 51 50 52 107, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +145: [23:09:57] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 65 64 60 61, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +145: [23:09:57] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 50 52 53 54, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +145: [23:09:57] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 58 59 60 61, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +145: [23:09:57] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 5 4 62 63, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 27 22 20 21, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 33 30 28 29, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 42 36 34 35, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 49 45 43 44, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 66 67 75 76, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 84 85 90 91, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 96 97 105 106, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 145: ----------- -145: [02:22:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 10 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 14 12 11 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 4 3 2 1, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -145: [02:22:57] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 16 15 14 12, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -145: [02:22:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 10 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 12 11 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 5 4 3 2, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 17 16 15 14, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 0 1 2 3, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 13 12 14 15, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 4 6 7 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -145: [02:22:57] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 6 7 8 9, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -145: [02:22:57] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 7 8 9 10, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -145: [02:22:57] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 4 6 16 17, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] -145: [02:22:57] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 7 6 4 5, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] -139: [02:22:57] Rep: 0 Mol:15 -139: [02:22:57] Rep: 0 Mol:19 +145: [23:09:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 10 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 14 12 11 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 4 3 2 1, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +145: [23:09:57] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 16 15 14 12, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +145: [23:09:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 10 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 12 11 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 5 4 3 2, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 17 16 15 14, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 0 1 2 3, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 13 12 14 15, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 4 6 7 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +145: [23:09:57] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 6 7 8 9, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +145: [23:09:57] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 7 8 9 10, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +145: [23:09:57] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 4 6 16 17, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] +145: [23:09:57] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 7 6 4 5, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] 145: ----------- -145: [02:22:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 13 14 16 3, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 10 12 13 14, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -145: [02:22:57] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 11 10 12 13, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 15 14 13 12, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 13 14 16 3, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 10 12 13 14, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +145: [23:09:57] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 11 10 12 13, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 15 14 13 12, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] 145: ----------- 145: ----------- -145: [02:22:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 15 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 3 5 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 8 7 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 11 13 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 17 16 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 20 22 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 15 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 3 5 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 8 7 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 11 13 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 17 16 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -145: [02:22:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 20 22 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -139: [02:22:57] Rep: 0 Mol:20 -139: [02:22:57] Rep: 0 Mol:23 -145: [02:22:57] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 0 1 2 3, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -145: [02:22:57] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 4 3 2 1, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -145: [02:22:57] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 9 8 10 11, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -145: [02:22:57] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 12 11 10 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -145: [02:22:57] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 18 17 19 20, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -145: [02:22:57] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 21 20 19 17, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -139: [02:22:57] Rep: 0 Mol:27 -139: [02:22:57] Rep: 0 Mol:31 -141: processing -141: launch :0 -141: launch :1 -141: launch :2 -141: launch :3 -141: [02:22:57] Rep: 0 Mol:3 -141: [02:22:57] Rep: 0 Mol:0 -141: [02:22:57] Rep: 0 Mol:4 -139: [02:22:57] Rep: 0 Mol:24 -141: [02:22:57] Rep: 0 Mol:1 -141: [02:22:57] Rep: 0 Mol:5 -141: [02:22:57] Rep: 0 Mol:9 -141: [02:22:57] Rep: 0 Mol:13 -141: [02:22:57] Rep: 0 Mol:2 -141: [02:22:57] Rep: 0 Mol:8 -141: [02:22:57] Rep: 0 Mol:17 -139: [02:22:57] Rep: 0 Mol:28 -141: [02:22:57] Rep: 0 Mol:7 -141: [02:22:57] Rep: 0 Mol:12 -141: [02:22:57] Rep: 0 Mol:11 -141: [02:22:57] Rep: 0 Mol:16 -141: [02:22:57] Rep: 0 Mol:15 -141: [02:22:57] Rep: 0 Mol:19 -141: [02:22:57] Rep: 0 Mol:20 -141: [02:22:57] Rep: 0 Mol:23 -141: [02:22:57] Rep: 0 Mol:27 -141: [02:22:57] Rep: 0 Mol:6 -139: [02:22:57] Rep: 20 Mol:1 -139: [02:22:57] Rep: 20 Mol:5 -139: [02:22:57] Rep: 20 Mol:9 -139: [02:22:57] Rep: 20 Mol:13 -139: [02:22:57] Rep: 20 Mol:17 -139: [02:22:57] Rep: 0 Mol:14 -139: [02:22:57] Rep: 20 Mol:21 -139: [02:22:57] Rep: 20 Mol:25 -139: [02:22:57] Rep: 20 Mol:29 -141: [02:22:57] Rep: 0 Mol:24 -141: [02:22:57] Rep: 0 Mol:28 -141: [02:22:57] Rep: 0 Mol:10 -141: [02:22:57] Rep: 0 Mol:21 -141: [02:22:57] Rep: 0 Mol:31 -141: [02:22:57] Rep: 0 Mol:25 -141: [02:22:57] Rep: 0 Mol:29 -139: [02:22:57] Rep: 0 Mol:18 -145: [02:22:57] UFFTYPER: Unrecognized atom type: Pt5+2 (1) -141: [02:22:57] Rep: 0 Mol:14 -145: [02:22:57] UFFTYPER: Unrecognized charge state for atom: 1 -141: [02:22:57] Rep: 0 Mol:18 -145: [02:22:57] UFFTYPER: Unrecognized charge state for atom: 1 -145: [02:22:57] UFFTYPER: Unrecognized charge state for atom: 1 -139: [02:22:57] Rep: 0 Mol:22 -141: [02:22:57] Rep: 0 Mol:22 -141: [02:22:57] Rep: 0 Mol:26 -141: [02:22:57] Rep: 0 Mol:30 -139: [02:22:57] Rep: 0 Mol:26 -139: [02:22:58] Rep: 0 Mol:30 -139: [02:22:58] Rep: 40 Mol:1 -139: [02:22:58] Rep: 40 Mol:5 -139: [02:22:58] Rep: 40 Mol:9 -139: [02:22:58] Rep: 40 Mol:13 -139: [02:22:58] Rep: 40 Mol:17 -139: [02:22:58] Rep: 40 Mol:21 -139: [02:22:58] Rep: 40 Mol:25 -139: [02:22:58] Rep: 40 Mol:29 -145: [02:22:58] UFFTYPER: Unrecognized charge state for atom: 5 -145: [02:22:58] UFFTYPER: Unrecognized charge state for atom: 5 -145: [02:22:58] UFFTYPER: Unrecognized charge state for atom: 5 -145: [02:22:58] UFFTYPER: Unrecognized charge state for atom: 6 -145: [02:22:58] UFFTYPER: Unrecognized charge state for atom: 6 -139: [02:22:58] Rep: 20 Mol:3 -139: [02:22:58] Rep: 20 Mol:7 -139: [02:22:58] Rep: 20 Mol:11 -139: [02:22:58] Rep: 20 Mol:15 -139: [02:22:58] Rep: 20 Mol:19 -145: [02:22:58] UFFTYPER: Unrecognized charge state for atom: 6 -139: [02:22:58] Rep: 20 Mol:23 -139: [02:22:58] Rep: 20 Mol:27 -139: [02:22:58] Rep: 20 Mol:31 -143: [02:22:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [02:22:58] Molecule does not have explicit Hs. Consider calling AddHs() -143: [02:22:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [02:22:58] Molecule does not have explicit Hs. Consider calling AddHs() -143: [02:22:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [02:22:58] Molecule does not have explicit Hs. Consider calling AddHs() -143: [02:22:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [02:22:58] Molecule does not have explicit Hs. Consider calling AddHs() -143: [02:22:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [02:22:58] Molecule does not have explicit Hs. Consider calling AddHs() -143: ..[02:22:58] Molecule does not have explicit Hs. Consider calling AddHs() -143: [02:22:58] Molecule does not have explicit Hs. Consider calling AddHs() -143: .[02:22:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [02:22:58] Molecule does not have explicit Hs. Consider calling AddHs() -143: .[02:22:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [02:22:58] Molecule does not have explicit Hs. Consider calling AddHs() -139: [02:22:58] Rep: 60 Mol:1 -139: [02:22:58] Rep: 60 Mol:5 -139: [02:22:58] Rep: 60 Mol:9 -139: [02:22:58] Rep: 60 Mol:13 -139: [02:22:58] Rep: 60 Mol:17 -139: [02:22:58] Rep: 60 Mol:21 -139: [02:22:58] Rep: 60 Mol:25 -139: [02:22:58] Rep: 60 Mol:29 -139: [02:22:58] Rep: 20 Mol:0 -139: [02:22:58] Rep: 20 Mol:4 -139: [02:22:58] Rep: 20 Mol:8 -139: [02:22:58] Rep: 20 Mol:12 -139: [02:22:58] Rep: 20 Mol:16 -139: [02:22:58] Rep: 20 Mol:20 -141: [02:22:58] Rep: 100 Mol:3 -141: [02:22:58] Rep: 100 Mol:7 -141: [02:22:58] Rep: 100 Mol:11 -141: [02:22:58] Rep: 100 Mol:15 -141: [02:22:58] Rep: 100 Mol:19 -141: [02:22:58] Rep: 100 Mol:23 -139: [02:22:58] Rep: 20 Mol:24 -139: [02:22:58] Rep: 20 Mol:28 -143: .[02:22:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [02:22:58] Molecule does not have explicit Hs. Consider calling AddHs() -141: [02:22:58] Rep: 100 Mol:27 -141: [02:22:58] Rep: 100 Mol:31 -143: .[02:22:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [02:22:58] Molecule does not have explicit Hs. Consider calling AddHs() -143: .[02:22:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [02:22:58] Molecule does not have explicit Hs. Consider calling AddHs() -143: .[02:22:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [02:22:58] Molecule does not have explicit Hs. Consider calling AddHs() -143: .[02:22:58] UFFTYPER: Unrecognized hybridization for atom: 0 -143: [02:22:58] UFFTYPER: Unrecognized atom type: Cu+1 (0) -143: .[02:22:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [02:22:58] Molecule does not have explicit Hs. Consider calling AddHs() -143: [02:22:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [02:22:58] Molecule does not have explicit Hs. Consider calling AddHs() -143: [02:22:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [02:22:58] Molecule does not have explicit Hs. Consider calling AddHs() -143: [02:22:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [02:22:58] Molecule does not have explicit Hs. Consider calling AddHs() -143: [02:22:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [02:22:58] Molecule does not have explicit Hs. Consider calling AddHs() -143: .[02:22:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [02:22:58] Molecule does not have explicit Hs. Consider calling AddHs() -143: .[02:22:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [02:22:58] Molecule does not have explicit Hs. Consider calling AddHs() -143: .[02:22:58] Molecule does not have explicit Hs. Consider calling AddHs() -143: [02:22:58] Molecule does not have explicit Hs. Consider calling AddHs() -143: ...[02:22:58] Molecule does not have explicit Hs. Consider calling AddHs() -143: [02:22:58] Molecule does not have explicit Hs. Consider calling AddHs() -143: [02:22:58] Molecule does not have explicit Hs. Consider calling AddHs() -141: [02:22:58] Rep: 100 Mol:0 -141: [02:22:58] Rep: 100 Mol:4 -141: [02:22:58] Rep: 100 Mol:8 -141: [02:22:58] Rep: 100 Mol:12 -141: [02:22:58] Rep: 100 Mol:16 -141: [02:22:58] Rep: 100 Mol:20 -141: [02:22:58] Rep: 100 Mol:24 -141: [02:22:58] Rep: 100 Mol:28 -139: [02:22:58] Rep: 40 Mol:3 -139: [02:22:58] Rep: 40 Mol:7 -141: [02:22:58] Rep: 100 Mol:1 -141: [02:22:58] Rep: 100 Mol:5 -141: [02:22:58] Rep: 100 Mol:9 -141: [02:22:58] Rep: 100 Mol:13 -143: ... -143: ---------------------------------------------------------------------- -143: Ran 19 tests in 0.319s -143: -143: OK -141: [02:22:58] Rep: 100 Mol:17 -141: [02:22:58] Rep: 100 Mol:21 -141: [02:22:58] Rep: 100 Mol:25 -141: [02:22:58] Rep: 100 Mol:29 -139: [02:22:58] Rep: 40 Mol:11 -139: [02:22:58] Rep: 40 Mol:15 -139: [02:22:58] Rep: 40 Mol:19 -139: [02:22:58] Rep: 40 Mol:23 -139: [02:22:58] Rep: 40 Mol:27 -139: [02:22:58] Rep: 40 Mol:31 -139: [02:22:58] Rep: 20 Mol:2 -139: [02:22:58] Rep: 20 Mol:6 -139: [02:22:58] Rep: 20 Mol:10 -139: [02:22:58] Rep: 20 Mol:14 -139: [02:22:58] Rep: 20 Mol:18 -139: [02:22:58] Rep: 20 Mol:22 -139: [02:22:58] Rep: 20 Mol:26 -139: [02:22:58] Rep: 20 Mol:30 -139: [02:22:58] Rep: 80 Mol:1 -139: [02:22:58] Rep: 80 Mol:5 -139: [02:22:58] Rep: 80 Mol:9 -139: [02:22:58] Rep: 80 Mol:13 -139: [02:22:58] Rep: 80 Mol:17 -139: [02:22:58] Rep: 80 Mol:21 -139: [02:22:58] Rep: 80 Mol:25 -139: [02:22:58] Rep: 80 Mol:29 -139: [02:22:58] Rep: 40 Mol:0 -139: [02:22:58] Rep: 40 Mol:4 -139: [02:22:58] Rep: 40 Mol:8 -139: [02:22:58] Rep: 40 Mol:12 -139: [02:22:58] Rep: 40 Mol:16 -139: [02:22:58] Rep: 40 Mol:20 -139: [02:22:58] Rep: 40 Mol:24 -139: [02:22:58] Rep: 40 Mol:28 -134/230 Test #143: pyForceFieldHelpers .................... Passed 1.30 sec +145: [23:09:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 15 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 3 5 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 8 7 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 11 13 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 17 16 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 20 22 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 15 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 3 5 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 8 7 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 11 13 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 17 16 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 20 22 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +145: [23:09:57] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 0 1 2 3, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +145: [23:09:57] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 4 3 2 1, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +145: [23:09:57] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 9 8 10 11, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +145: [23:09:57] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 12 11 10 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +145: [23:09:57] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 18 17 19 20, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +145: [23:09:57] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 21 20 19 17, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +145: [23:09:57] UFFTYPER: Unrecognized atom type: Pt5+2 (1) +145: [23:09:57] UFFTYPER: Unrecognized charge state for atom: 1 +145: [23:09:57] UFFTYPER: Unrecognized charge state for atom: 1 +145: [23:09:57] UFFTYPER: Unrecognized charge state for atom: 1 +139: [23:09:57] done +139: [23:09:57] ------------------------------------- +139: [23:09:57] Test MMFF multithreading2 +145: [23:09:57] UFFTYPER: Unrecognized charge state for atom: 5 +145: [23:09:57] UFFTYPER: Unrecognized charge state for atom: 5 +145: [23:09:57] UFFTYPER: Unrecognized charge state for atom: 5 +145: [23:09:58] UFFTYPER: Unrecognized charge state for atom: 6 +141: [23:09:58] done +141: [23:09:58] ------------------------------------- +141: [23:09:58] Testing GitHubIssue62. +141: [23:09:58] beta-lactam 39.6387 +141: [23:09:58] cyclopropanone 174.698 +141: [23:09:58] aziridine 337.986 +141: [23:09:58] aziridinone 115.248 +141: [23:09:58] isobutene 2.48217 +141: [23:09:58] acetone 1.91788 +141: [23:09:58] cyclopentanone 10.1648 +141: [23:09:58] cyclopropene 99.4921 +141: [23:09:58] cyclobutene 41.0156 +141: [23:09:58] cyclopropane 267.236 +145: [23:09:58] UFFTYPER: Unrecognized charge state for atom: 6 +141: [23:09:58] gamma-lactam 15.7471 +141: [23:09:58] trans-2,3-diphenylcyclopropan-1-one 203.398 +145: [23:09:58] UFFTYPER: Unrecognized charge state for atom: 6 +141: [23:09:58] cis-2,3-diphenylcyclopropan-1-one 206.852 +141: [23:09:58] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 +141: [23:09:58] cyclopropylidencyclobutane 218.879 +144: [23:09:55] --------------------------------- +144: [23:09:55] test3 +144: +144: [23:09:55] --------------------------------- +144: [23:09:55] test4 +144: +144: [23:09:55] --------------------------------- +144: [23:09:55] test5 +144: +144: [23:09:58] --------------------------------- +144: [23:09:58] test6 +144: +144: [23:09:58] --------------------------------- +144: [23:09:58] test15Dists +144: +144: [23:09:58] --------------------------------- +144: [23:09:58] test Issue 215 +144: +144: [23:09:58] --------------------------------- +144: [23:09:58] testMultipleConfs +144: +144: [23:09:58] --------------------------------- +144: [23:09:58] testMultipleConfsExpTors +144: +144: [23:09:58] --------------------------------- +144: [23:09:58] testIssue227 +144: +144: [23:09:58] --------------------------------- +144: [23:09:58] testIssue236 +144: +144: [23:09:58] --------------------------------- +144: [23:09:58] testOrdering +144: +144: [23:09:58] --------------------------------- +144: [23:09:58] testIssue244 +144: +144: [23:09:58] --------------------------------- +144: [23:09:58] testIssue251 +144: +144: [23:09:58] --------------------------------- +144: [23:09:58] testIssue276 +144: [23:09:58] --------------------------------- +144: [23:09:58] testIssue284 +144: +144: [23:09:58] --------------------------------- +144: [23:09:58] testIssue285 +144: +144: [23:09:58] --------------------------------- +144: [23:09:58] testIssue355 +144: +144: [23:09:58] --------------------------------- +144: [23:09:58] testRandomCoords +144: +144: [23:09:58] --------------------------------- +144: [23:09:58] test sf.net issue 1989539 +144: +144: [23:09:58] --------------------------------- +144: [23:09:58] test sf.net issue 2091864 +144: +144: [23:09:58] --------------------------------- +144: [23:09:58] test constrained embedding +144: +144: [23:09:58] ssd: 0.0752641 +144: [23:09:58] ssd: 0.0659363 +141: [23:09:58] diphenylmethylidencyclobutane 79.6139 +141: [23:09:58] done +141: [23:09:58] ------------------------------------- +141: [23:09:58] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. +141: [23:09:58] done +141: [23:09:58] ------------------------------------- +141: [23:09:58] Test square planar complexes +141: [23:09:58] done +141: [23:09:58] ------------------------------------- +141: [23:09:58] Test octahedral complexes +141: [23:09:58] done +134/230 Test #141: testUFFForceFieldHelpers ............... Passed 4.86 sec test 146 Start 146: pyDistGeomHelpers 146: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py" 146: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap 146: Test timeout computed to be: 1500 -139: [02:22:58] Rep: 60 Mol:3 -139: [02:22:58] Rep: 60 Mol:7 -139: [02:22:58] Rep: 60 Mol:11 -139: [02:22:58] Rep: 60 Mol:15 -139: [02:22:58] Rep: 60 Mol:19 -139: [02:22:58] Rep: 60 Mol:23 -139: [02:22:58] Rep: 60 Mol:27 -139: [02:22:58] Rep: 60 Mol:31 -145: [02:22:59] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -141: [02:22:59] Rep: 100 Mol:2 -141: [02:22:59] Rep: 100 Mol:6 -141: [02:22:59] Rep: 100 Mol:10 -141: [02:22:59] Rep: 100 Mol:14 -141: [02:22:59] Rep: 100 Mol:18 -141: [02:22:59] Rep: 100 Mol:22 -141: [02:22:59] Rep: 100 Mol:26 -141: [02:22:59] Rep: 100 Mol:30 -50: Randomness seeded to: 3503046925 -50: =============================================================================== -50: All tests passed (14835 assertions in 14 test cases) -50: -135/230 Test #50: canonTestsCatch ........................ Passed 12.84 sec +144: [23:09:58] --------------------------------- +144: [23:09:58] test sf.net issue 2091974 +144: +144: [23:09:58] --------------------------------- +144: [23:09:58] test sf.net issue 2835784 +144: +144: [23:09:58] --------------------------------- +144: [23:09:58] test sf.net issue 3019283 +144: +144: [23:09:58] --------------------------------- +144: [23:09:58] test sf.net issue 3238580 +144: +144: [23:09:58] --------------------------------- +144: [23:09:58] test sf.net issue 3483968 +144: +144: [23:09:58] --------------------------------- +144: [23:09:58] test github issue 55 +144: +144: [23:09:58] --------------------------------- +144: [23:09:58] test1 +144: +144: [23:09:58] --------------------------------- +144: [23:09:58] test multi-threading +144: +144: building molecules +144: generating reference data +27: Checking against /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +139: [23:09:58] done +139: [23:09:58] ------------------------------------- +139: [23:09:58] Test MMFF multithreading3 +27: All 191 tests passed +27: done +27: ------------------------------------- +27: Unit tests for all MMFF constraint terms. +27: 10.0003 +27: done +27: ------------------------------------- +27: Unit test for MMFF TorsionConstraint close to 0 degrees. +27: done +27: ------------------------------------- +27: Unit tests for copying MMFF ForceFields. +27: done +27: ------------------------------------- +27: Unit test for MMFF butane scan. +93: 0,0 0 +93: 0,1 0 +93: 1,0 0 +93: 1,1 0 +93: 2,0 0 +93: 2,1 0 +135/230 Test #93: testEnumeration ........................ Passed 20.15 sec test 147 Start 147: testMolAlign 147: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/testMolAlign 147: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign 147: Test timeout computed to be: 1500 -145: [02:22:59] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -139: [02:22:59] Rep: 60 Mol:0 -139: [02:22:59] Rep: 60 Mol:4 +146: .[23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: ..[23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: ..[23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: .[23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +147: *********************************************************** +147: Testing MolAlign +147: --------------------------------- +147: test1MolAlign +147: +147: --------------------------------- +147: test1GetBestRMS +147: +147: --------------------------------- +147: test1MolWithQueryAlign +147: +147: --------------------------------- +147: test2AtomMap +147: +147: --------------------------------- +147: test3Weights +147: +147: --------------------------------- +147: testIssue241 +147: +147: *********************************************************** +136/230 Test #147: testMolAlign ........................... Passed 0.25 sec +test 148 + Start 148: testO3AAlign + +148: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/testO3AAlign +148: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign +148: Test timeout computed to be: 1500 +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +139: [23:09:59] done +139: [23:09:59] ------------------------------------- +139: [23:09:59] Testing github 162: Incorrect SMILES after MMFF parameterization . +139: [23:09:59] done +139: [23:09:59] ------------------------------------- +139: [23:09:59] Testing github 224: crash during MMFF parameterization . +139: [23:09:59] done +139: [23:09:59] ------------------------------------- +139: [23:09:59] Testing github6728: crash due to missing stretch-bend params. +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +137/230 Test #139: testMMFFForceFieldHelpers .............. Passed 6.28 sec +test 149 + Start 149: molAlignCatchTest + +149: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/molAlignCatchTest +149: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign +149: Test timeout computed to be: 1500 +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +27: done +138/230 Test #27: testMMFFForceField ..................... Passed 29.83 sec +test 150 + Start 150: pyMolAlign + +150: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign/Wrap/testMolAlign.py" +150: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/Wrap +150: Test timeout computed to be: 1500 +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +149: Randomness seeded to: 2378330015 +149: 70420470 +149: 75192457 +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:10:00] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:10:00] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:10:00] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:10:00] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:10:00] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:10:00] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:10:00] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:10:00] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:10:00] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:10:00] Molecule does not have explicit Hs. Consider calling AddHs() +146: .[23:10:00] Molecule does not have explicit Hs. Consider calling AddHs() +145: [23:10:00] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +145: [23:10:00] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +146: [23:10:00] Molecule does not have explicit Hs. Consider calling AddHs() +145: [23:10:00] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +145: [23:10:01] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +145: [23:10:01] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +145: [23:10:01] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +146: [23:10:01] Molecule does not have explicit Hs. Consider calling AddHs() 124: Warning: Atom Count for residue GLU5A does not match expected count 124: Warning: Atom Count for residue ASN39A does not match expected count 124: Warning: Atom Count for residue GLU53A does not match expected count 124: Warning: Atom Count for residue ARG64A does not match expected count 124: Warning: Atom Count for residue LYS80A does not match expected count -139: [02:22:59] Rep: 80 Mol:3 -139: [02:22:59] Rep: 80 Mol:7 -139: [02:22:59] Rep: 80 Mol:11 -139: [02:22:59] Rep: 80 Mol:15 -139: [02:22:59] Rep: 80 Mol:19 -139: [02:22:59] Rep: 80 Mol:23 -139: [02:22:59] Rep: 80 Mol:27 -139: [02:22:59] Rep: 80 Mol:31 +123: Warning: Atom Count for residue GLU5A does not match expected count +123: Warning: Atom Count for residue ASN39A does not match expected count 124: Warning: Atom Count for residue GLU150A does not match expected count 124: Warning: Atom Count for residue ASN157A does not match expected count -139: [02:22:59] Rep: 60 Mol:8 -139: [02:22:59] Rep: 60 Mol:12 -139: [02:22:59] Rep: 60 Mol:16 -139: [02:22:59] Rep: 60 Mol:20 -139: [02:22:59] Rep: 60 Mol:24 -139: [02:22:59] Rep: 60 Mol:28 -139: [02:22:59] Rep: 40 Mol:2 -139: [02:22:59] Rep: 40 Mol:6 -139: [02:22:59] Rep: 40 Mol:10 -139: [02:22:59] Rep: 40 Mol:14 -139: [02:22:59] Rep: 40 Mol:18 -139: [02:22:59] Rep: 40 Mol:22 -124: .[02:22:59] DEPRECATION WARNING: please use MorganGenerator -124: .[02:22:59] DEPRECATION WARNING: please use MorganGenerator -124: ..[02:22:59] DEPRECATION WARNING: please use AtomPairGenerator -124: [02:22:59] DEPRECATION WARNING: please use AtomPairGenerator -124: [02:22:59] DEPRECATION WARNING: please use AtomPairGenerator -124: [02:22:59] DEPRECATION WARNING: please use AtomPairGenerator -124: [02:22:59] DEPRECATION WARNING: please use AtomPairGenerator -124: [02:22:59] DEPRECATION WARNING: please use AtomPairGenerator -124: .[02:22:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [02:22:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: ...[02:22:59] DEPRECATION WARNING: please use MorganGenerator -124: [02:22:59] DEPRECATION WARNING: please use MorganGenerator -124: [02:22:59] DEPRECATION WARNING: please use MorganGenerator -124: [02:22:59] DEPRECATION WARNING: please use MorganGenerator -124: [02:22:59] DEPRECATION WARNING: please use MorganGenerator -124: [02:22:59] DEPRECATION WARNING: please use MorganGenerator -124: [02:22:59] DEPRECATION WARNING: please use MorganGenerator -124: [02:22:59] DEPRECATION WARNING: please use MorganGenerator -124: [02:22:59] DEPRECATION WARNING: please use MorganGenerator -124: [02:22:59] DEPRECATION WARNING: please use MorganGenerator -124: [02:22:59] DEPRECATION WARNING: please use MorganGenerator -124: [02:22:59] DEPRECATION WARNING: please use MorganGenerator -124: [02:22:59] DEPRECATION WARNING: please use MorganGenerator -124: [02:22:59] DEPRECATION WARNING: please use MorganGenerator -124: [02:22:59] DEPRECATION WARNING: please use MorganGenerator -124: [02:22:59] DEPRECATION WARNING: please use MorganGenerator -124: [02:22:59] DEPRECATION WARNING: please use MorganGenerator -124: [02:22:59] DEPRECATION WARNING: please use MorganGenerator -124: [02:22:59] DEPRECATION WARNING: please use MorganGenerator -124: [02:22:59] DEPRECATION WARNING: please use MorganGenerator -124: [02:22:59] DEPRECATION WARNING: please use MorganGenerator -124: [02:22:59] DEPRECATION WARNING: please use MorganGenerator -139: [02:22:59] Rep: 40 Mol:26 -139: [02:22:59] Rep: 40 Mol:30 -124: ....[02:22:59] DEPRECATION WARNING: please use AtomPairGenerator -124: [02:22:59] DEPRECATION WARNING: please use AtomPairGenerator -124: ....[02:22:59] DEPRECATION WARNING: please use AtomPairGenerator -124: [02:22:59] DEPRECATION WARNING: please use AtomPairGenerator -124: .[02:22:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [02:22:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [02:22:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [02:22:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [02:22:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: ..[02:22:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [02:22:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [02:22:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [02:22:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [02:22:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [02:22:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: .[02:22:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -124: [02:22:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator +123: Warning: Atom Count for residue GLU53A does not match expected count +123: Warning: Atom Count for residue ARG64A does not match expected count +123: Warning: Atom Count for residue LYS80A does not match expected count +124: .[23:10:01] DEPRECATION WARNING: please use MorganGenerator +124: .[23:10:01] DEPRECATION WARNING: please use MorganGenerator +124: ..[23:10:01] DEPRECATION WARNING: please use AtomPairGenerator +124: [23:10:01] DEPRECATION WARNING: please use AtomPairGenerator +124: [23:10:01] DEPRECATION WARNING: please use AtomPairGenerator +124: [23:10:01] DEPRECATION WARNING: please use AtomPairGenerator +124: [23:10:01] DEPRECATION WARNING: please use AtomPairGenerator +124: [23:10:01] DEPRECATION WARNING: please use AtomPairGenerator +124: .[23:10:01] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [23:10:01] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: ...[23:10:01] DEPRECATION WARNING: please use MorganGenerator +124: [23:10:01] DEPRECATION WARNING: please use MorganGenerator +124: [23:10:01] DEPRECATION WARNING: please use MorganGenerator +124: [23:10:01] DEPRECATION WARNING: please use MorganGenerator +124: [23:10:01] DEPRECATION WARNING: please use MorganGenerator +124: [23:10:01] DEPRECATION WARNING: please use MorganGenerator +124: [23:10:01] DEPRECATION WARNING: please use MorganGenerator +124: [23:10:01] DEPRECATION WARNING: please use MorganGenerator +124: [23:10:01] DEPRECATION WARNING: please use MorganGenerator +124: [23:10:01] DEPRECATION WARNING: please use MorganGenerator +124: [23:10:01] DEPRECATION WARNING: please use MorganGenerator +124: [23:10:01] DEPRECATION WARNING: please use MorganGenerator +124: [23:10:01] DEPRECATION WARNING: please use MorganGenerator +124: [23:10:01] DEPRECATION WARNING: please use MorganGenerator +124: [23:10:01] DEPRECATION WARNING: please use MorganGenerator +124: [23:10:01] DEPRECATION WARNING: please use MorganGenerator +124: [23:10:01] DEPRECATION WARNING: please use MorganGenerator +124: [23:10:01] DEPRECATION WARNING: please use MorganGenerator +124: [23:10:01] DEPRECATION WARNING: please use MorganGenerator +124: [23:10:01] DEPRECATION WARNING: please use MorganGenerator +124: [23:10:01] DEPRECATION WARNING: please use MorganGenerator +124: [23:10:01] DEPRECATION WARNING: please use MorganGenerator +124: ....[23:10:01] DEPRECATION WARNING: please use AtomPairGenerator +124: [23:10:01] DEPRECATION WARNING: please use AtomPairGenerator +123: Warning: Atom Count for residue GLU150A does not match expected count +123: Warning: Atom Count for residue ASN157A does not match expected count +124: ....[23:10:01] DEPRECATION WARNING: please use AtomPairGenerator +124: [23:10:01] DEPRECATION WARNING: please use AtomPairGenerator +124: .[23:10:01] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [23:10:01] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [23:10:01] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [23:10:01] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [23:10:01] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: ..[23:10:01] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [23:10:01] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [23:10:01] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [23:10:01] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [23:10:01] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [23:10:01] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: .[23:10:01] DEPRECATION WARNING: please use TopologicalTorsionGenerator +124: [23:10:01] DEPRECATION WARNING: please use TopologicalTorsionGenerator 124: ... 124: ---------------------------------------------------------------------- -124: Ran 31 tests in 4.780s +124: Ran 31 tests in 12.135s 124: 124: OK 124: exactmw 78.046950192 @@ -27740,433 +28151,68 @@ 124: Phi 0.9130327103921437 124: exactmw 78.046950192 124: lipinskiHBA 0.0 -145: [02:22:59] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -136/230 Test #124: pyMolDescriptors ....................... Passed 5.46 sec -test 148 - Start 148: testO3AAlign - -148: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/testO3AAlign -148: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign -148: Test timeout computed to be: 1500 -147: *********************************************************** -147: Testing MolAlign -147: --------------------------------- -147: test1MolAlign -147: -147: --------------------------------- -147: test1GetBestRMS -147: -147: --------------------------------- -147: test1MolWithQueryAlign -147: -147: --------------------------------- -147: test2AtomMap -147: -147: --------------------------------- -147: test3Weights -147: -147: --------------------------------- -147: testIssue241 -147: -147: *********************************************************** -137/230 Test #147: testMolAlign ........................... Passed 0.18 sec -test 149 - Start 149: molAlignCatchTest - -149: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/molAlignCatchTest -149: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign -149: Test timeout computed to be: 1500 -145: [02:22:59] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -145: [02:22:59] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -145: [02:22:59] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -146: .[02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -149: Randomness seeded to: 816596561 -149: 73863120 -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: ..[02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: ..[02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: .[02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -149: 83959400 -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -139: [02:22:59] Rep: 80 Mol:0 -139: [02:22:59] Rep: 80 Mol:4 -139: [02:22:59] Rep: 80 Mol:8 -139: [02:22:59] Rep: 80 Mol:12 -139: [02:22:59] Rep: 80 Mol:16 -139: [02:22:59] Rep: 80 Mol:20 -139: [02:22:59] Rep: 80 Mol:24 -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -139: [02:22:59] Rep: 80 Mol:28 -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -126: [02:22:59] done -126: [02:22:59] ------------------------------------- -126: [02:22:59] Test GitHub Issue 258: Bad pattern fingerprint for query molecule -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -126: [02:22:59] done -126: [02:22:59] ------------------------------------- -126: [02:22:59] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -126: [02:22:59] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:59] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:59] done -126: [02:22:59] ------------------------------------- -126: [02:22:59] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -126: [02:22:59] done -126: [02:22:59] ------------------------------------- -126: [02:22:59] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -126: [02:22:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:59] done -126: [02:22:59] ------------------------------------- -126: [02:22:59] Test unfolded version of RDKFP -126: [02:22:59] ------------------------------------- -126: [02:22:59] Test bitinfo of RDKFP -126: 562: [ 2 ], -126: 709: [ 0 1 ], -126: 1118: [ 0 1 2 ], -126: 1183: [ 1 2 ], -126: 1233: [ 0 1 2 ], -126: 1308: [ 0 ], [ 1 ], -126: 1339: [ 2 ], -126: 1728: [ 1 2 ], -126: 1772: [ 0 ], [ 1 ], -126: 1813: [ 0 1 ], -126: ------------ -126: [02:22:59] ------------------------------------- -126: [02:22:59] Single atoms setting radius 1 bits in Morgan fingerprints -126: [02:22:59] done -126: [02:22:59] ------------------------------------- -126: [02:22:59] Github #879: Pattern fingerprint should set bits for single-atom fragments. -126: [02:22:59] done -126: [02:22:59] ------------------------------------- -126: [02:22:59] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms -126: [02:22:59] done -126: [02:22:59] ------------------------------------- -126: [02:22:59] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False -126: [02:22:59] done -126: [02:22:59] ------------------------------------- -126: [02:22:59] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called -126: [02:22:59] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:59] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:59] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:59] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:59] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:59] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:59] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:59] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:59] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:59] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:59] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:59] DEPRECATION WARNING: please use AtomPairGenerator -126: [02:22:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:59] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [02:22:59] done -126: [02:22:59] ------------------------------------- -126: [02:22:59] Github #2115: BitInfo not complete for RDKFingerprint -126: [02:22:59] done -126: [02:22:59] ------------------------------------- -126: [02:22:59] Github #3723: Fingerprint crash for mols with Zero order bonds -126: [02:22:59] done -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -139: [02:22:59] Rep: 60 Mol:2 -139: [02:22:59] Rep: 60 Mol:6 -139: [02:22:59] Rep: 60 Mol:10 -139: [02:22:59] Rep: 60 Mol:14 -139: [02:22:59] Rep: 60 Mol:18 -139: [02:22:59] Rep: 60 Mol:22 -139: [02:22:59] Rep: 60 Mol:26 -138/230 Test #126: testFingerprints ....................... Passed 5.07 sec -test 150 - Start 150: pyMolAlign - -150: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolAlign/Wrap/testMolAlign.py" -150: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/Wrap -150: Test timeout computed to be: 1500 -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -139: [02:22:59] Rep: 60 Mol:30 -141: [02:22:59] done -141: [02:22:59] ------------------------------------- -141: [02:22:59] Test UFF multithreading2 -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -144: [02:22:57] --------------------------------- -144: [02:22:57] test3 -144: -144: [02:22:57] --------------------------------- -144: [02:22:57] test4 -144: -144: [02:22:57] --------------------------------- -144: [02:22:57] test5 -144: -144: [02:22:59] --------------------------------- -144: [02:22:59] test6 -144: -144: [02:22:59] --------------------------------- -144: [02:22:59] test15Dists -144: -144: [02:22:59] --------------------------------- -144: [02:22:59] test Issue 215 -144: -144: [02:22:59] --------------------------------- -144: [02:22:59] testMultipleConfs -144: -144: [02:22:59] --------------------------------- -144: [02:22:59] testMultipleConfsExpTors -144: -144: [02:22:59] --------------------------------- -144: [02:22:59] testIssue227 -144: -144: [02:22:59] --------------------------------- -144: [02:22:59] testIssue236 -144: -144: [02:22:59] --------------------------------- -144: [02:22:59] testOrdering -144: -144: [02:22:59] --------------------------------- -144: [02:22:59] testIssue244 -144: -144: [02:22:59] --------------------------------- -144: [02:22:59] testIssue251 -144: -144: [02:22:59] --------------------------------- -144: [02:22:59] testIssue276 -144: [02:22:59] --------------------------------- -144: [02:22:59] testIssue284 -144: -144: [02:22:59] --------------------------------- -144: [02:22:59] testIssue285 -144: -144: [02:22:59] --------------------------------- -144: [02:22:59] testIssue355 -144: -144: [02:22:59] --------------------------------- -144: [02:22:59] testRandomCoords -144: -144: [02:22:59] --------------------------------- -144: [02:22:59] test sf.net issue 1989539 -144: -144: [02:22:59] --------------------------------- -144: [02:22:59] test sf.net issue 2091864 -144: -144: [02:22:59] --------------------------------- -144: [02:22:59] test constrained embedding -144: -144: [02:22:59] ssd: 0.0752641 -144: [02:22:59] ssd: 0.0659363 -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:22:59] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:23:00] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:23:00] Molecule does not have explicit Hs. Consider calling AddHs() -139: [02:23:00] Rep: 80 Mol:2 -139: [02:23:00] Rep: 80 Mol:6 -139: [02:23:00] Rep: 80 Mol:10 -139: [02:23:00] Rep: 80 Mol:14 -139: [02:23:00] Rep: 80 Mol:18 -139: [02:23:00] Rep: 80 Mol:22 -139: [02:23:00] Rep: 80 Mol:26 -139: [02:23:00] Rep: 80 Mol:30 -146: [02:23:00] Molecule does not have explicit Hs. Consider calling AddHs() -144: [02:22:59] --------------------------------- -144: [02:22:59] test sf.net issue 2091974 -144: -144: [02:22:59] --------------------------------- -144: [02:22:59] test sf.net issue 2835784 -144: -144: [02:22:59] --------------------------------- -144: [02:22:59] test sf.net issue 3019283 -144: -144: [02:22:59] --------------------------------- -144: [02:22:59] test sf.net issue 3238580 -144: -144: [02:22:59] --------------------------------- -144: [02:22:59] test sf.net issue 3483968 -144: -144: [02:23:00] --------------------------------- -144: [02:23:00] test github issue 55 -144: -144: [02:23:00] --------------------------------- -144: [02:23:00] test1 -144: -144: [02:23:00] --------------------------------- -144: [02:23:00] test multi-threading -144: -144: building molecules -144: generating reference data -146: [02:23:00] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:23:00] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:23:00] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:23:00] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:23:00] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:23:00] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:23:00] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:23:00] Molecule does not have explicit Hs. Consider calling AddHs() -139: [02:23:00] done -139: [02:23:00] ------------------------------------- -139: [02:23:00] Test MMFF multithreading2 -146: .[02:23:00] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:23:00] Molecule does not have explicit Hs. Consider calling AddHs() -141: [02:23:01] done -141: [02:23:01] ------------------------------------- -141: [02:23:01] Test UFF multithreading3 -146: [02:23:01] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:23:01] Molecule does not have explicit Hs. Consider calling AddHs() -139: [02:23:01] done -139: [02:23:01] ------------------------------------- -139: [02:23:01] Test MMFF multithreading3 -146: [02:23:01] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:23:02] Molecule does not have explicit Hs. Consider calling AddHs() -141: [02:23:02] done -141: [02:23:02] ------------------------------------- -141: [02:23:02] Testing GitHubIssue62. -141: [02:23:02] beta-lactam 39.6387 -141: [02:23:02] cyclopropanone 174.698 -141: [02:23:02] aziridine 337.986 -141: [02:23:02] aziridinone 115.248 -141: [02:23:02] isobutene 2.48217 -141: [02:23:02] acetone 1.91788 -141: [02:23:02] cyclopentanone 10.1648 -141: [02:23:02] cyclopropene 99.4921 -141: [02:23:02] cyclobutene 41.0156 -141: [02:23:02] cyclopropane 267.236 -141: [02:23:02] gamma-lactam 15.7471 -141: [02:23:02] trans-2,3-diphenylcyclopropan-1-one 203.398 -141: [02:23:02] cis-2,3-diphenylcyclopropan-1-one 206.852 -141: [02:23:02] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 -141: [02:23:02] cyclopropylidencyclobutane 218.879 -141: [02:23:02] diphenylmethylidencyclobutane 79.6139 -141: [02:23:02] done -141: [02:23:02] ------------------------------------- -141: [02:23:02] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. -141: [02:23:02] done -141: [02:23:02] ------------------------------------- -141: [02:23:02] Test square planar complexes -141: [02:23:02] done -141: [02:23:02] ------------------------------------- -141: [02:23:02] Test octahedral complexes -141: [02:23:02] done -139/230 Test #141: testUFFForceFieldHelpers ............... Passed 5.71 sec +139/230 Test #124: pyMolDescriptors ....................... Passed 13.53 sec test 151 Start 151: testFeatures 151: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 151: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures 151: Test timeout computed to be: 1500 -151: [02:23:02] ------------------------------------- -151: [02:23:02] AtomType parser testing. -151: [02:23:02] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] -151: [02:23:02] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]' -151: [02:23:02] done -151: [02:23:02] ------------------------------------- -151: [02:23:02] FeatureDefinition parser testing. -151: [02:23:02] done -151: [02:23:02] ------------------------------------- -151: [02:23:02] Test pulling feat defs from a string. -151: [02:23:02] done -151: [02:23:02] ------------------------------------- -151: [02:23:02] FeatureDef functionality testing. -151: [02:23:02] done -151: [02:23:02] ------------------------------------- -151: [02:23:02] FeatureFactory testing. -151: [02:23:02] 1 -151: [02:23:02] 2 -151: [02:23:02] 3 -151: [02:23:02] 4 -151: [02:23:02] 5 -151: [02:23:02] 6 -151: [02:23:02] done -151: [02:23:02] ------------------------------------- -151: [02:23:02] Feature Location testing. -151: [02:23:02] done -151: [02:23:02] ------------------------------------- -151: [02:23:02] Test building a FeatureFactory from a file -151: [02:23:02] done -151: [02:23:02] ------------------------------------- -151: [02:23:02] Testing Issue 224. -151: [02:23:02] done -151: [02:23:02] ------------------------------------- -151: [02:23:02] Testing Issue 225. -151: [02:23:02] done -151: [02:23:02] ------------------------------------- -151: [02:23:02] Test Issue346 -151: [02:23:02] done -151: [02:23:02] ------------------------------------- -151: [02:23:02] Test Issue347 -151: [02:23:02] done -151: [02:23:02] ------------------------------------- -151: [02:23:02] Testing Issue 348. -151: [02:23:02] SMARTS Parse Error: syntax error while parsing: [C[C] -151: [02:23:02] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' -151: [02:23:02] ------------------------------------- -151: [02:23:02] Testing Nested AtomType definitions. +151: [23:10:01] ------------------------------------- +151: [23:10:01] AtomType parser testing. +151: [23:10:01] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] +151: [23:10:01] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]' +151: [23:10:01] done +151: [23:10:01] ------------------------------------- +151: [23:10:01] FeatureDefinition parser testing. +151: [23:10:01] done +151: [23:10:01] ------------------------------------- +151: [23:10:01] Test pulling feat defs from a string. +151: [23:10:01] done +151: [23:10:01] ------------------------------------- +151: [23:10:01] FeatureDef functionality testing. +123: =============================================================================== +123: All tests passed (515 assertions in 10 test cases) +123: +151: [23:10:01] done +151: [23:10:01] ------------------------------------- +151: [23:10:01] FeatureFactory testing. +151: [23:10:01] 1 +151: [23:10:01] 2 +151: [23:10:01] 3 +151: [23:10:01] 4 +151: [23:10:01] 5 +151: [23:10:01] 6 +151: [23:10:01] done +151: [23:10:01] ------------------------------------- +151: [23:10:01] Feature Location testing. +151: [23:10:01] done +151: [23:10:01] ------------------------------------- +151: [23:10:01] Test building a FeatureFactory from a file +151: [23:10:01] done +151: [23:10:01] ------------------------------------- +151: [23:10:01] Testing Issue 224. +151: [23:10:01] done +151: [23:10:01] ------------------------------------- +151: [23:10:01] Testing Issue 225. +151: [23:10:01] done +151: [23:10:01] ------------------------------------- +151: [23:10:01] Test Issue346 +151: [23:10:01] done +151: [23:10:01] ------------------------------------- +151: [23:10:01] Test Issue347 +151: [23:10:01] done +151: [23:10:01] ------------------------------------- +151: [23:10:01] Testing Issue 348. +151: [23:10:01] SMARTS Parse Error: syntax error while parsing: [C[C] +151: [23:10:01] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' +151: [23:10:01] ------------------------------------- +151: [23:10:01] Testing Nested AtomType definitions. 151: [$([$([$([C;!$(C=[O,N,P,S]);!$(C#N)]),c]);R])] -151: [02:23:02] ------------------------------------- -151: [02:23:02] Testing Github Issue #252: crash when calling getPos() with no conformer. -151: [02:23:02] expect a precondition failure message below -151: [02:23:02] +151: [23:10:01] ------------------------------------- +151: [23:10:01] Testing Github Issue #252: crash when calling getPos() with no conformer. +151: [23:10:01] expect a precondition failure message below +151: [23:10:01] 151: 151: **** 151: Pre-condition Violation @@ -28179,43 +28225,33 @@ 151: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 151: 2# RDKit::MolChemicalFeature::getPos(int) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1 151: 3# RDKit::MolChemicalFeature::getPos() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1 -151: 4# 0x0000AAAAD1F81790 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures -151: 5# 0x0000AAAAD1F74208 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures -151: 6# 0x0000FFFF938B229C in /lib/aarch64-linux-gnu/libc.so.6 +151: 4# 0x0000AAAAE1291790 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +151: 5# 0x0000AAAAE1284208 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +151: 6# 0x0000FFFF9231229C in /lib/aarch64-linux-gnu/libc.so.6 151: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -151: 8# 0x0000AAAAD1F743B0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +151: 8# 0x0000AAAAE12843B0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 151: ---------- 151: **** 151: -151: [02:23:02] Done -151: [02:23:02] ------------------------------------- -151: [02:23:02] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() -151: [02:23:02] done -140/230 Test #151: testFeatures ........................... Passed 0.03 sec +151: [23:10:01] Done +151: [23:10:01] ------------------------------------- +151: [23:10:01] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() +151: [23:10:01] done +140/230 Test #151: testFeatures ........................... Passed 0.04 sec test 152 Start 152: pyChemicalFeatures 152: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py" 152: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap 152: Test timeout computed to be: 1500 -149: 3673467320 -27: Checking against /build/reproducible-path/rdkit-202409.2/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -139: [02:23:03] done -139: [02:23:03] ------------------------------------- -139: [02:23:03] Testing github 162: Incorrect SMILES after MMFF parameterization . -139: [02:23:03] done -139: [02:23:03] ------------------------------------- -139: [02:23:03] Testing github 224: crash during MMFF parameterization . -139: [02:23:03] done -139: [02:23:03] ------------------------------------- -139: [02:23:03] Testing github6728: crash due to missing stretch-bend params. -141/230 Test #139: testMMFFForceFieldHelpers .............. Passed 6.40 sec +141/230 Test #123: descriptorsTestCatch ................... Passed 13.75 sec test 153 Start 153: testShapeHelpers 153: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers/testShapeHelpers 153: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers 153: Test timeout computed to be: 1500 +146: [23:10:01] Molecule does not have explicit Hs. Consider calling AddHs() 153: *********************************************************** 153: Testing ShapeHelpers 153: --------------------------------- @@ -28228,7 +28264,7 @@ 153: testGithub4364 153: 153: *********************************************************** -142/230 Test #153: testShapeHelpers ....................... Passed 0.05 sec +142/230 Test #153: testShapeHelpers ....................... Passed 0.10 sec test 154 Start 154: pyShapeHelpers @@ -28236,88 +28272,63 @@ 154: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap 154: Test timeout computed to be: 1500 144: validating reference data -146: [02:23:03] Molecule does not have explicit Hs. Consider calling AddHs() -152: .[02:23:03] Molecule does not have explicit Hs. Consider calling AddHs() -152: .[02:23:03] Molecule does not have explicit Hs. Consider calling AddHs() -152: ..[02:23:03] Molecule does not have explicit Hs. Consider calling AddHs() -152: .[02:23:03] Molecule does not have explicit Hs. Consider calling AddHs() -152: .[02:23:03] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] -152: [02:23:03] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' +146: [23:10:02] Molecule does not have explicit Hs. Consider calling AddHs() +152: .[23:10:02] Molecule does not have explicit Hs. Consider calling AddHs() +152: .[23:10:02] Molecule does not have explicit Hs. Consider calling AddHs() +149: 2662640408 +152: ..[23:10:02] Molecule does not have explicit Hs. Consider calling AddHs() +152: .[23:10:02] Molecule does not have explicit Hs. Consider calling AddHs() +152: .[23:10:02] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] +152: [23:10:02] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' 152: ... 152: ---------------------------------------------------------------------- -152: Ran 9 tests in 0.128s +152: Ran 9 tests in 0.289s 152: 152: OK -27: All 191 tests passed -27: done -27: ------------------------------------- -27: Unit tests for all MMFF constraint terms. -27: 10.0003 -27: done -27: ------------------------------------- -27: Unit test for MMFF TorsionConstraint close to 0 degrees. -27: done -27: ------------------------------------- -27: Unit tests for copying MMFF ForceFields. -143/230 Test #152: pyChemicalFeatures ..................... Passed 0.89 sec +146: [23:10:02] Molecule does not have explicit Hs. Consider calling AddHs() +154: . +154: ---------------------------------------------------------------------- +154: Ran 1 test in 0.119s +154: +154: OK +154: Testing Shape Helpers wrapper +143/230 Test #154: pyShapeHelpers ......................... Passed 1.20 sec test 155 Start 155: testMolCatalog 155: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/testMolCatalog 155: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog 155: Test timeout computed to be: 1500 -27: done -27: ------------------------------------- -27: Unit test for MMFF butane scan. -144/230 Test #155: testMolCatalog ......................... Passed 0.05 sec +144/230 Test #155: testMolCatalog ......................... Passed 0.06 sec test 156 Start 156: pyMolCatalog 156: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolCatalog/Wrap/rough_test.py" 156: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/Wrap 156: Test timeout computed to be: 1500 -146: [02:23:03] Molecule does not have explicit Hs. Consider calling AddHs() -27: done -145/230 Test #27: testMMFFForceField ..................... Passed 18.40 sec +145/230 Test #152: pyChemicalFeatures ..................... Passed 1.53 sec test 157 Start 157: moldraw2DTest1 157: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTest1 157: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D 157: Test timeout computed to be: 1500 -157: ----------------- Test 1 -123: Warning: Atom Count for residue GLU5A does not match expected count -123: Warning: Atom Count for residue ASN39A does not match expected count -123: Warning: Atom Count for residue GLU53A does not match expected count -123: Warning: Atom Count for residue ARG64A does not match expected count -123: Warning: Atom Count for residue LYS80A does not match expected count -123: Warning: Atom Count for residue GLU150A does not match expected count -123: Warning: Atom Count for residue ASN157A does not match expected count -154: . -154: ---------------------------------------------------------------------- -154: Ran 1 test in 0.131s -154: -154: OK -154: Testing Shape Helpers wrapper -157: file test1_6.svg gave hash 1109656969U not the expected 2635907956U -157: Done -157: ----------------- Test 2 -157: file test2_1.png gave hash 3244109893U not the expected 307437906U -156: . -156: ---------------------------------------------------------------------- -156: Ran 1 test in 0.009s -156: -156: OK -123: =============================================================================== -123: All tests passed (515 assertions in 10 test cases) -123: -146/230 Test #123: descriptorsTestCatch ................... Passed 10.33 sec +50: Randomness seeded to: 1032273499 +50: =============================================================================== +50: All tests passed (14835 assertions in 14 test cases) +50: +146/230 Test #50: canonTestsCatch ........................ Passed 31.73 sec test 158 Start 158: moldraw2DTestCatch 158: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 158: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D 158: Test timeout computed to be: 1500 +157: ----------------- Test 1 +157: file test1_6.svg gave hash 1109656969U not the expected 2635907956U +157: Done +157: ----------------- Test 2 +157: file test2_1.png gave hash 3244109893U not the expected 307437906U 157: file test2_2.png gave hash 1653770192U not the expected 610424244U 157: file test2_3.png gave hash 2294574389U not the expected 2179746375U 157: Done @@ -28326,128 +28337,130 @@ 157: Done 157: ----------------- Test 5 157: file test5_1.png gave hash 3301334295U not the expected 1269428339U -147/230 Test #156: pyMolCatalog ........................... Passed 0.38 sec -test 159 - Start 159: moldraw2DRxnTest1 - -159: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DRxnTest1 -159: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D -159: Test timeout computed to be: 1500 157: file test5_2.png gave hash 792995950U not the expected 3073694291U -158: Randomness seeded to: 2396676435 -158: file contourMol_1.svg gave hash 4125787245U not the expected 2604538953U -158: file contourMol_2.svg gave hash 2761342533U not the expected 572669511U 157: file test5_3.png gave hash 3533595670U not the expected 1865192682U 157: Done 157: ----------------- Test 6 (atom labels) -159: ----------------- Test 1 -158: file contourMol_3.svg gave hash 1333854566U not the expected 936771429U -149: 867918400 -149: =============================================================================== -149: All tests passed (73 assertions in 3 test cases) -149: -158: file contourMol_4.svg gave hash 4249475618U not the expected 3302971362U 157: Done 157: ----------------- Test 7 (backgrounds) -158: file contourMol_5.svg gave hash 3376179346U not the expected 2230414999U 157: file test7_1.png gave hash 2930913537U not the expected 3033050306U -159: file rxn_test1_1.png gave hash 2385318368U not the expected 1556334749U -146: [02:23:04] Molecule does not have explicit Hs. Consider calling AddHs() 157: file test7_2.png gave hash 1226546555U not the expected 3476380724U 157: Done 157: ----------------- Test8: PrepareMolDrawing +158: Randomness seeded to: 660923727 +158: file contourMol_1.svg gave hash 4125787245U not the expected 2604538953U 157: Done 157: ----------------- Test multi-threaded drawing 157: reading molecules -148/230 Test #149: molAlignCatchTest ...................... Passed 4.89 sec -test 160 - Start 160: pyMolDraw2D +158: file contourMol_2.svg gave hash 2761342533U not the expected 572669511U +157: generating reference drawings +149: 916463963 +149: =============================================================================== +149: All tests passed (73 assertions in 3 test cases) +149: +147/230 Test #149: molAlignCatchTest ...................... Passed 3.93 sec +test 159 + Start 159: moldraw2DRxnTest1 -160: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py" -160: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap -160: Test timeout computed to be: 1500 +159: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DRxnTest1 +159: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D +159: Test timeout computed to be: 1500 +158: file contourMol_3.svg gave hash 1333854566U not the expected 936771429U +158: file contourMol_4.svg gave hash 4249475618U not the expected 3302971362U +158: file contourMol_5.svg gave hash 3376179346U not the expected 2230414999U +159: ----------------- Test 1 158: file testGithub3226_1.png gave hash 3169002270U not the expected 2350054896U 158: file testGithub3226_2.png gave hash 2453613824U not the expected 606206725U -159: file rxn_test1_2.png gave hash 2554855195U not the expected 1924084263U -159: file rxn_test1_3.png gave hash 2471407454U not the expected 1644921059U +159: file rxn_test1_1.png gave hash 2385318368U not the expected 1556334749U +157: processing +157: launch :0 +157: launch :1 +157: launch :2 +157: launch :3 158: file testGithub3226_3.png gave hash 2178685661U not the expected 2282880418U 158: file testPNGMetadata_1.png gave hash 1114763408U not the expected 2423299691U +159: file rxn_test1_2.png gave hash 2554855195U not the expected 1924084263U +158: file testPNGMetadata_2.png gave hash 831235773U not the expected 2803353117U +156: . +156: ---------------------------------------------------------------------- +156: Ran 1 test in 0.035s +156: +156: OK +159: file rxn_test1_3.png gave hash 2471407454U not the expected 1644921059U +146: [23:10:03] Molecule does not have explicit Hs. Consider calling AddHs() 159: file rxn_test1_4.png gave hash 3424511197U not the expected 2471435686U -157: generating reference drawings 159: file rxn_test1_5.png gave hash 583013587U not the expected 1428782307U -158: file testPNGMetadata_2.png gave hash 831235773U not the expected 2803353117U 159: file rxn_test1_6.png gave hash 2508294714U not the expected 483353696U +158: [23:10:04] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +158: [23:10:04] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +146: [23:10:04] Molecule does not have explicit Hs. Consider calling AddHs() +158: file testHandDrawn-1.svg gave hash 1143910631U not the expected 2253418236U +158: [23:10:04] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +158: [23:10:04] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. 159: file rxn_test1_7.png gave hash 699575715U not the expected 528963379U 159: Done 159: ----------------- Test 2: some examples that caused problems in testing +158: file testHandDrawn-1.png gave hash 3641551470U not the expected 698316547U 159: file rxn_test2_1.png gave hash 1690240778U not the expected 399415052U -158: [02:23:04] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -158: [02:23:04] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +148/230 Test #156: pyMolCatalog ........................... Passed 1.12 sec +test 160 + Start 160: pyMolDraw2D + +160: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py" +160: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap +160: Test timeout computed to be: 1500 159: 3 [cH:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1>>CC(C)[c:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1 CN1CCC(CC1)N(C)S(=O)(=O)c2ccccc2 CC(C)c1ccc(cc1)S(=O)(=O)N(C)C2CCN(CC2)C -158: file testHandDrawn-1.svg gave hash 1143910631U not the expected 2253418236U -158: [02:23:04] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -158: [02:23:04] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. 159: file rxn_test2_2_1.png gave hash 3463090055U not the expected 1215378243U 159: 3 [cH:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1>>[cH:3]1[cH:2][c:1]([cH:6][cH:5][c:4]1)Cl Cc1cccc(c1C)N2CCN(CC2)CCCNC(=O)c3cc([nH]c3C)c4ccccc4 Cc1cccc(c1C)N2CCN(CC2)CCCNC(=O)c3cc([nH]c3C)c4ccc(cc4)Cl +158: [23:10:04] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +158: [23:10:04] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. 159: file rxn_test2_2_2.png gave hash 3677922459U not the expected 3645141778U -158: file testHandDrawn-1.png gave hash 3641551470U not the expected 698316547U 159: 2 Cc1c(cc([nH]1)[c:1]2[cH:2][cH:3][cH:4][cH:5][cH:6]2)[C:7](=[O:8])[NH:9][CH2:10][CH2:11]>>CCc1nc(c(n1[c:1]2[cH:2][cH:3][cH:4][cH:5][cH:6]2)C)[C:7](=[O:8])[NH:9][CH2:10][CH2:11] Cc1c(cc([nH]1)c2ccccc2)C(=O)NCCN3CCN(C 159: 2 C3)c4cccc(c4Cl)Cl CCc1nc(c(n1c2ccccc2)C)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl 159: 3 [c:1][C:2](=[O:3])[NH:4]CCC[CH2:5][N:6]([CH2:7])[CH2:8]>>[c:1][C:2](=[O:3])[NH:4]C[CH2:5][N:6]([CH2:7])[CH2:8] CCCn1c(c(cc1c2ccccc2)C(=O)NCCCCN3CCN(CC3)c4cccc(c4Cl)Cl)C CCCn1c(c(cc1c2ccccc2)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl)C +158: file testHandDrawn-2.svg gave hash 700659102U not the expected 4132716144U +158: [23:10:04] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +158: [23:10:04] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. 159: file rxn_test2_2_3.png gave hash 95245485U not the expected 551946805U 159: 3 [CH3:1]c1c(cc(n1[CH3:2])C(C)(C)C)[C:3]>>[CH3:2]c1c(c(nc(n1)[CH3:1])[C:3])OC Cc1cccc(c1C)N2CCN(CC2)CCNC(=O)c3cc(n(c3C)C)C(C)(C)C Cc1cccc(c1C)N2CCN(CC2)CCNC(=O)c3c(c(nc(n3)C)C)OC -149/230 Test #154: pyShapeHelpers ......................... Passed 1.00 sec -test 161 - Start 161: testFMCS - -161: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/testFMCS -161: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FMCS -161: Test timeout computed to be: 1500 -157: processing -157: launch :0 -157: launch :1 -157: launch :2 -157: launch :3 -158: [02:23:04] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -158: [02:23:04] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. -158: file testHandDrawn-2.svg gave hash 700659102U not the expected 4132716144U -158: [02:23:04] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -158: [02:23:04] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +158: file testHandDrawn-2.png gave hash 1714651611U not the expected 1605553248U +158: [23:10:04] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +158: [23:10:04] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +158: file testHandDrawn-3.svg gave hash 2359787964U not the expected 4199337510U +158: [23:10:04] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +158: [23:10:04] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. 159: file rxn_test2_2_4.png gave hash 3468758430U not the expected 4234617566U 159: Done 159: ----------------- Test 3: test reactant highlighting -158: file testHandDrawn-2.png gave hash 1714651611U not the expected 1605553248U -158: [02:23:04] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -158: [02:23:04] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. -158: file testHandDrawn-3.svg gave hash 2359787964U not the expected 4199337510U -158: [02:23:04] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -158: [02:23:04] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. -159: file rxn_test3_1.png gave hash 2229288660U not the expected 4176857511U 158: file testHandDrawn-3.png gave hash 2770454011U not the expected 2881952238U -158: [02:23:04] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -158: [02:23:04] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +146: [23:10:04] Molecule does not have explicit Hs. Consider calling AddHs() +158: [23:10:04] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +158: [23:10:04] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. 158: file testHandDrawn-4.svg gave hash 1880974760U not the expected 4197407865U -158: [02:23:04] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -158: [02:23:04] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +158: [23:10:04] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +158: [23:10:04] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +158: file testHandDrawn-4.png gave hash 4013133897U not the expected 3431655453U +159: file rxn_test3_1.png gave hash 2229288660U not the expected 4176857511U 159: Done 159: ----------------- Test 4: some examples from SMARTS in testing 159: draw! -158: file testHandDrawn-4.png gave hash 4013133897U not the expected 3431655453U 159: file rxn_test4_1.png gave hash 1061176844U not the expected 4187207676U 159: done -146: [02:23:04] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:10:04] Molecule does not have explicit Hs. Consider calling AddHs() 159: file rxn_test4_2.png gave hash 3123925758U not the expected 3490081297U 159: Done -150/230 Test #159: moldraw2DRxnTest1 ...................... Passed 0.29 sec -test 162 - Start 162: pyFMCS +149/230 Test #159: moldraw2DRxnTest1 ...................... Passed 1.14 sec +test 161 + Start 161: testFMCS -162: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Wrap/testFMCS.py" -162: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Wrap -162: Test timeout computed to be: 1500 -160: ...[02:23:04] Font file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. -160: [02:23:04] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. -160: ..........[02:23:04] +161: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/testFMCS +161: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FMCS +161: Test timeout computed to be: 1500 +146: [23:10:04] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:10:05] Molecule does not have explicit Hs. Consider calling AddHs() +160: ...[23:10:05] Font file /build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. +160: [23:10:05] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +160: ..........[23:10:05] 160: 160: **** 160: Pre-condition Violation @@ -28461,7 +28474,7 @@ 160: 2# RDKit::prepMolForDrawing(RDKit::ROMol const*, bool, bool, bool, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/Draw/rdMolDraw2D.so 160: 3# boost::python::objects::caller_py_function_impl, boost::mpl::vector7 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/Draw/rdMolDraw2D.so 160: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -160: 5# 0x0000FFFFAC0315C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +160: 5# 0x0000FFFFB73C15C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 160: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 160: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 160: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so @@ -28472,17 +28485,17 @@ 160: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 160: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 160: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -160: 16# 0x0000FFFFAB774180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -160: 17# 0x0000FFFFAB774118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -160: 18# 0x0000FFFFAB7740A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -160: 19# 0x0000FFFFAB774040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -160: 20# 0x0000FFFFAB773FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +160: 16# 0x0000FFFFB6B04180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +160: 17# 0x0000FFFFB6B04118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +160: 18# 0x0000FFFFB6B040A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +160: 19# 0x0000FFFFB6B04040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +160: 20# 0x0000FFFFB6B03FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 160: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 160: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 160: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 160: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 160: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -160: 26# 0x0000FFFFAC02E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +160: 26# 0x0000FFFFB73BE19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 160: 27# _PyObject_MakeTpCall in /usr/bin/python3 160: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 160: 29# 0x00000000004C3D1C in /usr/bin/python3 @@ -28515,17 +28528,43 @@ 160: 56# _PyRun_AnyFileObject in /usr/bin/python3 160: 57# Py_RunMain in /usr/bin/python3 160: 58# Py_BytesMain in /usr/bin/python3 -160: 59# 0x0000FFFFAE47229C in /lib/aarch64-linux-gnu/libc.so.6 +160: 59# 0x0000FFFFB980229C in /lib/aarch64-linux-gnu/libc.so.6 160: 60# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 160: 61# _start in /usr/bin/python3 160: ---------- 160: **** 160: +160: ...................... +160: ---------------------------------------------------------------------- +160: Ran 35 tests in 0.582s +160: +160: OK +160: json lasso 144: processing 144: launch :0 144: launch :1 144: launch :2 144: launch :3 +150/230 Test #160: pyMolDraw2D ............................ Passed 1.92 sec +test 162 + Start 162: pyFMCS + +162: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/FMCS/Wrap/testFMCS.py" +162: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Wrap +162: Test timeout computed to be: 1500 +146: .[23:10:06] Molecule does not have explicit Hs. Consider calling AddHs() +158: file testHandDrawn-5a.svg gave hash 2986893714U not the expected 3628607349U +158: [23:10:06] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +158: [23:10:06] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +158: file testHandDrawn-5b.svg gave hash 3461999036U not the expected 2522138089U +158: [23:10:06] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. +158: [23:10:06] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. +158: file testHandDrawn-5.png gave hash 474833683U not the expected 3439548169U +158: file testBrackets-5a.svg gave hash 279553678U not the expected 3061667963U +158: file testSGroupData-3a.svg gave hash 62481132U not the expected 2405789536U +158: file testSGroupData-3a.svg gave hash 62481132U not the expected 2405789536U +158: file testPositionVariation-1b.svg gave hash 3055422087U not the expected 174339626U +158: [23:10:07] unrecognized bond typefile testGithub2976.svg gave hash 2858811732U not the expected 2669316911U 148: *********************************************************** 148: Testing O3AAlign 148: --------------------------------- @@ -28556,14 +28595,365 @@ 148: testMMFFO3A multithreading 148: 148: generating reference data -160: ...................... -160: ---------------------------------------------------------------------- -160: Ran 35 tests in 0.218s -160: -160: OK -160: json lasso -146: [02:23:04] Molecule does not have explicit Hs. Consider calling AddHs() -151/230 Test #160: pyMolDraw2D ............................ Passed 0.67 sec +158: file testGithub4238_1.png gave hash 457161194U not the expected 3410617836U +158: file testGithub4323_1.png gave hash 1351611338U not the expected 3723958844U +158: file testGithub4323_3.png gave hash 1010250572U not the expected 2185913679U +158: [23:10:08] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. +161: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds +161: Time elapsed 0.000 seconds +161: +161: test32() +161: MCS: [#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#6]=[#6]-[#6](-[#7]-[#6]1:[#6]:[#6](-[#16](-[#7]2-[#6]-[#6]-[#8]-[#6]-[#6]-2)(=[#8])=[#8]):[#6]:[#6]:[#6]:1-[#7](-[#6]-[#6])-[#6]-[#6])=[#8] 31 atoms, 33 bonds +161: Time elapsed 0.213 seconds +161: +161: test190() +161: MCS: [#6]1:[#6]:[#6]2:[#8]:[#6](:[#7]:[#6]:2:[#6]:[#6]:1)-[#6]1:[#6]:[#6](-[#7]-[#6](=[#8])-[#6]):[#6]:[#6]:[#6]:1 19 atoms, 21 bonds +161: Time elapsed 0.050 seconds +161: +161: test3() +161: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6]-[#6](=[#8])-[#7]-[#6]-[#6]-[#6]-[#6] 14 atoms, 14 bonds +161: Time elapsed 0.040 seconds +161: +161: testSimpleFast() +161: MCS: [#6]-[#8]-[#6]-[#6]1:[#6]:[#7]:[#6]:[#6](:[#6]:1):[#7]:[#6]1:[#6]:[#6]:[#6]:[#6](:[#6]:1)-[#8]-[#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#17] 24 atoms, 26 bonds +161: Time elapsed 0.264 seconds +161: +161: testSimple() +161: MCS: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds +161: Time elapsed 0.239 seconds +161: MCS MatchFusedRings: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds +161: Time elapsed 0.288 seconds +161: MCS MatchFusedRingsStrict: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds +161: Time elapsed 0.342 seconds +161: +161: testSegFault() +161: MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds +161: Time elapsed 0.025 seconds +161: MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds +161: Time elapsed 0.043 seconds +161: MCS MatchFusedRingsStrict: [#6;r6,!R1]1:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@1 6 atoms, 6 bonds +161: Time elapsed 0.043 seconds +161: +161: testThreshold() +161: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +161: Time elapsed 0.000 seconds +161: +161: testRing1() +161: MCS: [#6]-&!@[#8]-&!@[#6]-&!@[#6]1:&@[#6]:&@[#7]:&@[#6]:&@[#6]2:&@[#6]:&@1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#7]:&@2 16 atoms, 17 bonds +161: Time elapsed 0.864 seconds +161: MCS MatchFusedRings: [#6]-&!@[#8]-&!@[#6]-&!@[#6]1:&@[#6]:&@[#7]:&@[#6]:&@[#6]2:&@[#6]:&@1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#7]:&@2 16 atoms, 17 bonds +161: Time elapsed 0.496 seconds +161: MCS MatchFusedRingsStrict: [#6;r6,!R1]1:&@[#6;r6,!R1]:&@[#7;r6,!R1]:&@[#6;r6,!R1](:&@[#6]:&@[#6]:&@1)-&!@[#6](=&!@[#8])-&!@[#8]-&!@[#6](-&!@[#6])-&!@[#6] 12 atoms, 12 bonds +161: Time elapsed 0.479 seconds +161: +161: testAtomCompareIsotopes() +161: MCS: [0*]-[0*]-[13*] 3 atoms, 2 bonds +161: Time elapsed 0.000 seconds +161: +161: testAtomCompareAnyAtom() +161: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds +161: Time elapsed 0.000 seconds +161: +161: testAtomCompareAnyAtom() +161: MCS: [#6]1-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:1=,-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds +161: Time elapsed 0.000 seconds +161: +161: testAtomCompareAnyAtom() +161: MCS: [#1]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 8 atoms, 8 bonds +161: Time elapsed 0.000 seconds +161: +161: testAtomCompareAnyAtom() +161: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 7 atoms, 7 bonds +161: Time elapsed 0.000 seconds +161: +161: testJnk1LigandsDistance() +161: MCS: [#6]-[#6]-[#8]-[#6]1:[#6](:[#6](:[#6]:[#6](:[#7]:1)-[#7]-[#6](=[#8])-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1)-[#7])-[#6]#[#7] CCOc1nc(NC(=O)Cc2ccccc2)cc(N)c1C#N 22 atoms, 23 bonds +161: Time elapsed 0.010 seconds +161: MCS: [#6]-[#6]-[#8]-[#6]1:[#6](:[#6](:[#6]:[#6](:[#7]:1)-[#7]-[#6](=[#8])-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6](:[#6]:1)-[#6,#8])-[#7])-[#6]#[#7] *c1cccc(CC(=O)Nc2cc(N)c(C#N)c(OCC)n2)c1 23 atoms, 24 bonds +161: Time elapsed 0.001 seconds +161: +161: test18() +161: Query +MAP [CH3:0][c:1]1[n:2][c:3]([CH2:4][N:5]([CH:6]([CH3:7])[c:8]2[n:9][cH:10][cH:11][cH:12][cH:13]2)[CH2:14][CH2:15][CH2:16][CH2:17][NH2:18])[cH:19][cH:20][cH:21]1 +161: MCS: [#6](:[#7]:[#6]-[#6]-[#7](-[#6](-[#6])-[#6]1:[#7]:[#6]:[#6]:[#6]:[#6]:1)-[#6]-[#6]-[#6]-[#6]-[#7]):[#6]:[#6]:[#6] 21 atoms, 21 bonds +161: Time elapsed 0.004 seconds +161: +161: test504() +161: Query +MAP [CH2:0]([CH2:1][CH2:2][NH:3][C:4]([CH:5]1[CH2:6][CH:7]1[c:8]1[c:9][c:10]([Cl:11])[c:12]([Cl:13])[cH:14][c:15]1)=[O:16])[CH2:17][CH2:18][N:19]1[CH2:20][CH2:21][CH:22]([NH:23][C:24]([NH:25][c:26]2[cH:27][cH:28][c:29]([Cl:30])[cH:31][cH:32]2)=[O:33])[CH2:34]1 +161: MCS: [#6](-[#6]-[#6]-[#7]-[#6](-[#6]1-[#6]-[#6]-1-[#6]1:[#6]:[#6](-[#17]):[#6](:[#6]:[#6]:1)-[#17])=[#8])-[#6]-[#6]-[#7](-[#6]-[#6]-[#6]-[#7]-[#6](-[#7]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1)=[#8])-[#6] 34 atoms, 36 bonds +161: Time elapsed 0.327 seconds +161: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds +161: Time elapsed 0.001 seconds +161: MCS: [#6]1-[#6]-[#7]-[#6](-[#6]-[#7]-1-[#6]1:[#6](:[#6]:[#6]2:[#6](:[#6](:[#6]:[#7](-[#6]3-[#6]-[#6]-3):[#6]:2:[#6]:1)-[#6](=[#8])-[#8])=[#8])-[#9])-[#6] 25 atoms, 28 bonds +161: Time elapsed 0.076 seconds +161: Query Cc1c(F)c(N2CCNC(C)C2)cc2c1c(=O)c(C(=O)O)cn2C1CC1 26(26) atoms, 29(28) bonds +161: 1 Seeds:1 MCS 25 atoms, 28 bonds for 0.0011 seconds. bond[0]=6 +161: STATISTICS: +161: Total Growing Steps = 1, MCS found on 1 step, for 0.0011 seconds +161: Initial Seeds = 1, Mismatched 0 +161: Inspected Seeds = 2 +161: Rejected by BestSize = 0 +161: IndividualBondExcluded = 0 +161: MatchCheck Seeds = 2 +161: MatchCalls = 2 +161: MatchFound = 1 +161: fastMatchCalls = 1 +161: fastMatchFound = 0 +161: slowMatchCalls = 2 +161: slowMatchFound = 1 +161: DupCacheFound = 0 0 matched, 0 mismatched +161: HashCache size = 1 keys +161: HashCache size = 1 entries +161: FindHashInCache = 2 +161: HashFoundInCache= 0 +161: ExactMatchCalls = 0 +161: ExactMatchFound = 0 +161: Time elapsed 0.001 seconds +161: query=OCCl SubstructMatch(useChirality=false) res =1 size=3 +161: query=OCCl SubstructMatch(useChirality=true ) res =1 size=3 +161: test target = O[C@H](F)CCl query = C(F)C useChirality = 0 +161: res sub = 1 size=3 +161: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds +161: test target = O[C@H](F)CCl query = C(F)C useChirality = 1 +161: res sub = 1 size=3 +161: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds +161: test target = CC[C@H](F)Cl query = CCC useChirality = 0 +161: res sub = 1 size=3 +161: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +161: test target = CC[C@H](F)Cl query = CCC useChirality = 1 +161: res sub = 1 size=3 +161: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +161: test target = CCC(F)Cl query = CC useChirality = 0 +161: res sub = 1 size=2 +161: MCS: [#6]-[#6] 2 atoms, 1 bonds +161: test target = CCC(F)Cl query = CC useChirality = 1 +161: res sub = 1 size=2 +161: MCS: [#6]-[#6] 2 atoms, 1 bonds +161: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 0 +161: res sub = 1 size=4 +161: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +161: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 1 +161: res sub = 1 size=4 +161: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +161: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 0 +161: res sub = 1 size=4 +161: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +161: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 1 +161: res sub = 1 size=4 +161: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +161: test target = O[C@H](F)CCl query = CC(F)C useChirality = 0 +161: res sub = 0 size=0 +161: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds +161: test target = O[C@H](F)CCl query = CC(F)C useChirality = 1 +161: res sub = 0 size=0 +161: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds +161: test target = O[C@H](F)CCl query = OC(F)C useChirality = 0 +161: res sub = 1 size=4 +161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +161: test target = O[C@H](F)CCl query = OC(F)C useChirality = 1 +161: res sub = 1 size=4 +161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +161: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 0 +161: res sub = 1 size=4 +161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +161: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 1 +161: res sub = 1 size=4 +161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +161: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 0 +161: res sub = 1 size=4 +161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +161: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 1 +161: res sub = 0 size=0 +161: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +161: test target = OC(F)CCl query = OC(F)C useChirality = 0 +161: res sub = 1 size=4 +161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +161: test target = OC(F)CCl query = OC(F)C useChirality = 1 +161: res sub = 1 size=4 +161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +161: test target = OC(F)CCl query = O[C@H](F)C useChirality = 0 +161: res sub = 1 size=4 +161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +161: test target = OC(F)CCl query = O[C@H](F)C useChirality = 1 +161: res sub = 0 size=0 +161: MCS: [#9] 1 atoms, 0 bonds +161: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 0 +161: res sub = 1 size=4 +161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +161: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 1 +161: res sub = 0 size=0 +161: MCS: [#9] 1 atoms, 0 bonds +161: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 0 +161: res sub = 1 size=3 +161: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +161: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 1 +161: res sub = 1 size=3 +161: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +161: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 0 +161: res sub = 1 size=3 +161: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +161: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 1 +161: res sub = 1 size=3 +161: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +161: +161: 0. <<<<<<<<< actual MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds >>>>>>> +161: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 0 +161: res sub = 1 size=3 +161: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +161: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 1 +161: res sub = 1 size=3 +161: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +161: done +158: file testFlexiCanvas.2a.png gave hash 671825155U not the expected 3217758043U +158: file testFlexiCanvas.2b.png gave hash 822043607U not the expected 4070063910U +158: file testFlexiCanvas.3.svg gave hash 3867616289U not the expected 2819587550U +158: file testGithub4764.sz1.svg gave hash 2364628953U not the expected 3611125861U +158: file testGithub4764.sz2.svg gave hash 1490175526U not the expected 1936114454U +158: file testGithub4764.sz3.svg gave hash 1662881340U not the expected 2712214121U +158: file testGithub4764.sz1.png gave hash 4257427598U not the expected 98827714U +158: file testGithub4764.sz2.png gave hash 3003904136U not the expected 89252465U +158: file testGithub4764.sz3.png gave hash 2973487547U not the expected 148503574U +158: file testGithub_5061.svg gave hash 4026821599U not the expected 83338095U +158: file github5383_1.svg gave hash 2761342533U not the expected 3666750661U +158: file github5383_2.svg gave hash 2560846108U not the expected 0U +148: processing +148: launch :0 +148: launch :1 +148: launch :2 +148: launch :3 +158: file github5383_1.png gave hash 3989466152U not the expected 992803933U +158: file acs1996_1.png gave hash 1855954821U not the expected 2957839025U +158: file acs1996_2.svg gave hash 908745273U not the expected 1521279517U +158: file acs1996_2.png gave hash 307943157U not the expected 2664798808U +158: file acs1996_3.svg gave hash 510450189U not the expected 879041204U +158: file acs1996_5.svg gave hash 3624853279U not the expected 1680320774U +158: file acs1996_8.svg gave hash 3359655656U not the expected 2477908768U +158: file acs1996_9.svg gave hash 231896677U not the expected 3747924004U +158: file acs1996_10.svg gave hash 1008047306U not the expected 2229333301U +158: [23:10:09] ACS drawing mode works best with a flexiCanvas i.e. a drawer created with width and height of -1. The scale will be fixed, and that may not look great with a pre-determined size. +158: file bond_highlights_8.svg gave hash 1272407071U not the expected 2956924065U +158: file test_github5947.svg gave hash 737562322U not the expected 3122633523U +158: file test_github6112.svg gave hash 3291975047U not the expected 3278777629U +158: file test_github6200_1.svg gave hash 1975293465U not the expected 1044179149U +158: file github6336_1.png gave hash 1930712448U not the expected 2958833204U +158: file test_github6397_2.svg gave hash 2405824082U not the expected 3422233570U +158: file test_github6397_3.svg gave hash 759740391U not the expected 3320683230U +158: file test_github6397_4.svg gave hash 2454933776U not the expected 2960192928U +158: file test_github6397_5.svg gave hash 1843492326U not the expected 1245534660U +158: file github6504_1.svg gave hash 3649936662U not the expected 1429448598U +158: file github6504_2.svg gave hash 106020287U not the expected 2871662880U +158: file github6569_1.svg gave hash 1698514747U not the expected 116573839U +158: file github6569_2.svg gave hash 2778768241U not the expected 2367779037U +158: file AtropCanon1.svg gave hash 818325437U not the expected 526339583U +158: file AtropManyChiralsEnhanced.svg gave hash 292902747U not the expected 348414093U +158: file testGithub6968.svg gave hash 940962291U not the expected 1554428830U +158: file testWedgeNonSingleBonds-1.svg gave hash 2116685919U not the expected 865601717U +158: file testWedgeNonSingleBonds-2.svg gave hash 1174395532U not the expected 2960559495U +158: file testWedgeNonSingleBonds-3.svg gave hash 2542970771U not the expected 1428196589U +158: file testWedgeNonSingleBonds-4.svg gave hash 700876833U not the expected 3897680387U +158: file testWedgeNonSingleBonds-5.svg gave hash 2012191155U not the expected 2183530217U +158: file testWedgeNonSingleBonds-6.svg gave hash 2517061935U not the expected 238313010U +158: file testWedgeNonSingleBonds-7.svg gave hash 157069219U not the expected 3641456570U +158: file testWedgeNonSingleBonds-8.svg gave hash 3431784338U not the expected 3209701539U +158: file testWedgingShouldBeOnSingleBond.svg gave hash 2637422009U not the expected 1002741488U +158: file testHighlightHeteroAtoms_1.svg gave hash 4006401146U not the expected 1769258632U +158: file testHighlightHeteroAtoms_2.svg gave hash 1248188292U not the expected 893937335U +158: file testGithub_7739_1.svg gave hash 233164329U not the expected 52079325U +158: file testGithub_7739_3.svg gave hash 1653424667U not the expected 1126644226U +158: file testGithub_7739_4.svg gave hash 3214282623U not the expected 9844878U +158: [23:10:11] +158: +158: **** +158: Pre-condition Violation +158: +158: Violation occurred on line 206 in file ./Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.cpp +158: Failed Expression: atomIdx < atCds_.size() && atomIdx < atomLabels_.size() +158: ---------- +158: Stacktrace: +158: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +158: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +158: 2# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::calcSymbolEllipse(unsigned int, RDGeom::Point2D&, double&, double&) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +158: 3# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::makeAtomHighlights(std::vector >, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +158: 4# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::extractMCHighlights() in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +158: 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +158: 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +158: 7# RDKit::MolDraw2D::drawMoleculeWithHighlights(RDKit::ROMol const&, std::__cxx11::basic_string, std::allocator > const&, std::map >, std::less, std::allocator > > > > const&, std::map >, std::less, std::allocator > > > > const&, std::map, std::allocator > > const&, std::map, std::allocator > > const&, int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +158: 8# 0x0000AAAAC1614468 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 9# 0x0000AAAAC16DA1AC in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 10# 0x0000AAAAC16DAB60 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 11# 0x0000AAAAC16DAF94 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 12# 0x0000AAAAC16AF998 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 13# 0x0000AAAAC16AFEE4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 14# 0x0000AAAAC160DB10 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 15# 0x0000FFFFA463229C in /lib/aarch64-linux-gnu/libc.so.6 +158: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +158: 17# 0x0000AAAAC160DBF0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: ---------- +158: **** +158: +158: [23:10:11] +158: +158: **** +158: Range Error +158: idx +158: Violation occurred on line 329 in file ./Code/GraphMol/ROMol.cpp +158: Failed Expression: 2 < 0 +158: ---------- +158: Stacktrace: +158: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +158: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +158: 2# RDKit::ROMol::getBondWithIdx(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +158: 3# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::makeBondHighlights(std::vector >, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +158: 4# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::extractMCHighlights() in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +158: 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +158: 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +158: 7# RDKit::MolDraw2D::drawMoleculeWithHighlights(RDKit::ROMol const&, std::__cxx11::basic_string, std::allocator > const&, std::map >, std::less, std::allocator > > > > const&, std::map >, std::less, std::allocator > > > > const&, std::map, std::allocator > > const&, std::map, std::allocator > > const&, int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +158: 8# 0x0000AAAAC1613EAC in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 9# 0x0000AAAAC16DA1AC in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 10# 0x0000AAAAC16DAB60 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 11# 0x0000AAAAC16DAF94 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 12# 0x0000AAAAC16AF998 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 13# 0x0000AAAAC16AFEE4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 14# 0x0000AAAAC160DB10 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 15# 0x0000FFFFA463229C in /lib/aarch64-linux-gnu/libc.so.6 +158: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +158: 17# 0x0000AAAAC160DBF0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: ---------- +158: **** +158: +158: [23:10:11] +158: +158: **** +158: Range Error +158: idx +158: Violation occurred on line 329 in file ./Code/GraphMol/ROMol.cpp +158: Failed Expression: 0 < 0 +158: ---------- +158: Stacktrace: +158: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +158: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +158: 2# RDKit::ROMol::getBondWithIdx(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +158: 3# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::makeBondHighlights(std::vector >, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +158: 4# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::extractMCHighlights() in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +158: 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +158: 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +158: 7# RDKit::MolDraw2D::drawMoleculeWithHighlights(RDKit::ROMol const&, std::__cxx11::basic_string, std::allocator > const&, std::map >, std::less, std::allocator > > > > const&, std::map >, std::less, std::allocator > > > > const&, std::map, std::allocator > > const&, std::map, std::allocator > > const&, int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +158: 8# 0x0000AAAAC1614514 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 9# 0x0000AAAAC16DA1AC in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 10# 0x0000AAAAC16DAB60 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 11# 0x0000AAAAC16DAF94 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 12# 0x0000AAAAC16AF998 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 13# 0x0000AAAAC16AFEE4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 14# 0x0000AAAAC160DB10 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: 15# 0x0000FFFFA463229C in /lib/aarch64-linux-gnu/libc.so.6 +158: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +158: 17# 0x0000AAAAC160DBF0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +158: ---------- +158: **** +158: +158: =============================================================================== +158: All tests passed (6801 assertions in 105 test cases) +158: +151/230 Test #158: moldraw2DTestCatch ..................... Passed 8.59 sec test 163 Start 163: FMCStest @@ -30535,45 +30925,31 @@ 163: 163: testFileSDF_RandomSet(): benchmark/chembl13_threshold_90.smi 163: ERROR: RDKit could not load input file -152/230 Test #163: FMCStest ............................... Passed 0.06 sec +152/230 Test #163: FMCStest ............................... Passed 0.12 sec test 164 Start 164: molHashCatchTest 164: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/molHashCatchTest 164: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolHash 164: Test timeout computed to be: 1500 -164: Randomness seeded to: 1862920885 +164: Randomness seeded to: 2415649079 164: =============================================================================== 164: All tests passed (332 assertions in 13 test cases) 164: -153/230 Test #164: molHashCatchTest ....................... Passed 0.08 sec +153/230 Test #164: molHashCatchTest ....................... Passed 0.09 sec test 165 Start 165: pyMolHash 165: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolHash/Wrap/testMolHash.py" 165: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/Wrap 165: Test timeout computed to be: 1500 -146: [02:23:05] Molecule does not have explicit Hs. Consider calling AddHs() -158: file testHandDrawn-5a.svg gave hash 2986893714U not the expected 3628607349U -158: [02:23:05] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -158: [02:23:05] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. -158: file testHandDrawn-5b.svg gave hash 3461999036U not the expected 2522138089U -158: [02:23:05] Font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/ComicNeue-Regular.ttf not found. -158: [02:23:05] Falling back to original font file /build/reproducible-path/rdkit-202409.2/Data/Fonts/Telex-Regular.ttf. -158: file testHandDrawn-5.png gave hash 474833683U not the expected 3439548169U -158: file testBrackets-5a.svg gave hash 279553678U not the expected 3061667963U -158: file testSGroupData-3a.svg gave hash 62481132U not the expected 2405789536U -158: file testSGroupData-3a.svg gave hash 62481132U not the expected 2405789536U -158: file testPositionVariation-1b.svg gave hash 3055422087U not the expected 174339626U +161: [23:10:12] The provided InitialSeed is not an MCS and will be ignored 165: .... 165: ---------------------------------------------------------------------- -165: Ran 4 tests in 0.016s +165: Ran 4 tests in 0.028s 165: 165: OK -158: [02:23:05] unrecognized bond typefile testGithub2976.svg gave hash 2858811732U not the expected 2669316911U -158: file testGithub4238_1.png gave hash 457161194U not the expected 3410617836U -158: file testGithub4323_1.png gave hash 1351611338U not the expected 3723958844U -154/230 Test #165: pyMolHash .............................. Passed 0.51 sec +154/230 Test #165: pyMolHash .............................. Passed 0.93 sec test 166 Start 166: testMMPA @@ -30582,9 +30958,12 @@ 166: Test timeout computed to be: 1500 166: 166: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -166: Time elapsed 0.002280 seconds +166: Time elapsed 0.002283 seconds 166: 1: res= NULL,C[*:1].C[C:2](C(=O)Nc1ccccc1[*:1])[NH+]1CCCC1 166: 1: NOREF. Reference data NOT LISTED in test case. +162: ........................................[23:10:13] The provided InitialSeed is not an MCS and will be ignored +162: [23:10:13] The provided InitialSeed is not an MCS and will be ignored +162: [23:10:13] The provided InitialSeed is not an MCS and will be ignored 166: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1 166: 2: NOREF. Reference data NOT LISTED in test case. 166: 3: res= O=C(Nc1ccccc1[*:1])[*:2],C[*:1].C[C:3]([NH+]1CCCC1)[*:2] @@ -30619,11 +30998,14 @@ 166: 17: NOREF. Reference data NOT LISTED in test case. 166: 18: res= NULL,C1CC[NH+]([*:1])C1.Cc1ccccc1NC(=O)[C:2](C)[*:1] 166: 18: NOREF. Reference data NOT LISTED in test case. +162: .[23:10:13] The provided InitialSeed is not an MCS and will be ignored +162: [23:10:13] The provided InitialSeed is not an MCS and will be ignored +162: [23:10:13] The provided InitialSeed is not an MCS and will be ignored 166: 166: --- UNMATCHED Reference RESULTS: --- 166: 1: Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[*:1][C:7]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:2].Cc1ccccc1NC(=O)[*:1] 166: ----------------------------------- -166: Time elapsed 0.010135 seconds +166: Time elapsed 0.018251 seconds 166: 166: TEST 1 mol: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 166: 1: NULL, C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O @@ -30644,6 +31026,8 @@ 166: 8: NOREF. Reference data NOT LISTED in test case.O=C(NC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 166: 9: O=C(NCC[*:1])[*:2], Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1] 166: 9: NOREF. Reference data NOT LISTED in test case.O=C(NCC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1] +162: .[23:10:13] The provided InitialSeed is not an MCS and will be ignored +162: [23:10:13] The provided InitialSeed is not an MCS and will be ignored 166: 10: NULL, Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 166: 10: PASSED. matchedRefRes = 3 166: 11: C([*:1])[*:2], Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] @@ -30656,6 +31040,9 @@ 166: 14: PASSED. matchedRefRes = 11 166: 15: NULL, Cc1c(C(=O)NCC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:1] 166: 15: PASSED. matchedRefRes = 2 +162: [23:10:13] The provided InitialSeed is not an MCS and will be ignored +162: .[23:10:13] The provided InitialSeed is not an MCS and will be ignored +162: [23:10:13] The provided InitialSeed is not an MCS and will be ignored 166: 166: --- UNMATCHED Reference RESULTS: --- 166: 5: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,C([*:1])[*:2],Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2] @@ -30665,7 +31052,7 @@ 166: ----------------------------------- 166: 166: TEST mol: ZINC21984717 Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 -166: Time elapsed 0.002052 seconds +166: Time elapsed 0.018259 seconds 166: 1: res= NULL,C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O 166: 1: PASSED. matchedRefRes = 4 166: 2: res= O=[n+]1c([*:2])c([*:1])n([O-])c2ccccc21,C[*:1].O=C(NCCO)[*:2] @@ -30686,6 +31073,7 @@ 166: 9: NOREF. Reference data NOT LISTED in test case. 166: 10: res= NULL,Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 166: 10: PASSED. matchedRefRes = 3 +162: [23:10:13] The provided InitialSeed is not an MCS and will be ignored 166: 11: res= C([*:1])[*:2],Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 166: 11: NOREF. Reference data NOT LISTED in test case. 166: 12: res= C(C[*:2])[*:1],Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] @@ -30705,7 +31093,7 @@ 166: ----------------------------------- 166: 166: TEST mol: Case1-SIMPLE CC(N1CC1)C(=O) Case1-SIMPLE -166: Time elapsed 0.000552 seconds +166: Time elapsed 0.000598 seconds 166: 1: res= NULL,C[*:1].O=CC(N1CC1)[*:1] 166: 1: PASSED. matchedRefRes = 2 166: 2: res= O=CC([*:1])[*:2],C1CN1[*:2].C[*:1] @@ -30720,11 +31108,6 @@ 166: 6: NOREF. Reference data NOT LISTED in test case. 166: 7: res= NULL,CC(N1CC1)[*:1].O=C[*:1] 166: 7: PASSED. matchedRefRes = 7 -148: processing -148: launch :0 -148: launch :1 -148: launch :2 -148: launch :3 166: 166: --- UNMATCHED Reference RESULTS: --- 166: 1: CC(N1CC1)C(=O),Case1-SIMPLE,C([*:1])([*:2])[*:3],C1CN1[*:2].C[*:1].O=C[*:3] @@ -30732,7 +31115,7 @@ 166: ----------------------------------- 166: 166: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -166: Time elapsed 0.002900 seconds +166: Time elapsed 0.018481 seconds 166: 1: res= NULL,C[*:1].C[C:2](C(=O)Nc1ccccc1[*:1])[NH+]1CCCC1 166: 1: NOREF. Reference data NOT LISTED in test case. 166: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1 @@ -30775,7 +31158,7 @@ 166: ----------------------------------- 166: 166: TEST mol: Case2 O=C(OCc1ccccc1)C(O)c1ccccc1 Case2 -166: Time elapsed 0.002274 seconds +166: Time elapsed 0.014562 seconds 166: 1: res= NULL,O=C(O[*:1])C(O)c1ccccc1.c1ccc(C[*:1])cc1 166: 1: NOREF. Reference data NOT LISTED in test case. 166: 2: res= C([*:1])[*:2],O=C(O[*:1])C(O)c1ccccc1.c1ccc([*:2])cc1 @@ -30806,6 +31189,11 @@ 166: 14: PASSED. matchedRefRes = 1 166: 15: res= OC([*:1])[*:2],O=C(OCc1ccccc1)[*:1].c1ccc([*:2])cc1 166: 15: NOREF. Reference data NOT LISTED in test case. +162: ................. +162: ---------------------------------------------------------------------- +162: Ran 60 tests in 6.316s +162: +162: OK 166: 16: res= NULL,O=C(OCc1ccccc1)C(c1ccccc1)[*:1].O[*:1] 166: 16: NOREF. Reference data NOT LISTED in test case. 166: 17: res= O=C(OCc1ccccc1)C([*:1])[*:2],O[*:1].c1ccc([*:2])cc1 @@ -30816,466 +31204,32 @@ 166: --- ALL PASSED --- 166: ----------------------------------- 166: 5 TEST CASES FAILED -155/230 Test #166: testMMPA ............................... Passed 0.12 sec +155/230 Test #166: testMMPA ............................... Passed 0.33 sec test 167 Start 167: pyMMPA 167: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MMPA/Wrap/testMMPA.py" 167: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/Wrap 167: Test timeout computed to be: 1500 -158: file testGithub4323_3.png gave hash 1010250572U not the expected 2185913679U -158: [02:23:05] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. -158: file testFlexiCanvas.2a.png gave hash 671825155U not the expected 3217758043U -158: file testFlexiCanvas.2b.png gave hash 822043607U not the expected 4070063910U -158: file testFlexiCanvas.3.svg gave hash 3867616289U not the expected 2819587550U -158: file testGithub4764.sz1.svg gave hash 2364628953U not the expected 3611125861U -158: file testGithub4764.sz2.svg gave hash 1490175526U not the expected 1936114454U -158: file testGithub4764.sz3.svg gave hash 1662881340U not the expected 2712214121U -158: file testGithub4764.sz1.png gave hash 4257427598U not the expected 98827714U -146: .[02:23:06] Molecule does not have explicit Hs. Consider calling AddHs() -158: file testGithub4764.sz2.png gave hash 3003904136U not the expected 89252465U -158: file testGithub4764.sz3.png gave hash 2973487547U not the expected 148503574U -158: file testGithub_5061.svg gave hash 4026821599U not the expected 83338095U -158: file github5383_1.svg gave hash 2761342533U not the expected 3666750661U -158: file github5383_2.svg gave hash 2560846108U not the expected 0U -158: file github5383_1.png gave hash 3989466152U not the expected 992803933U -158: file acs1996_1.png gave hash 1855954821U not the expected 2957839025U -158: file acs1996_2.svg gave hash 908745273U not the expected 1521279517U -158: file acs1996_2.png gave hash 307943157U not the expected 2664798808U -158: file acs1996_3.svg gave hash 510450189U not the expected 879041204U -158: file acs1996_5.svg gave hash 3624853279U not the expected 1680320774U -158: file acs1996_8.svg gave hash 3359655656U not the expected 2477908768U -158: file acs1996_9.svg gave hash 231896677U not the expected 3747924004U -158: file acs1996_10.svg gave hash 1008047306U not the expected 2229333301U -158: [02:23:06] ACS drawing mode works best with a flexiCanvas i.e. a drawer created with width and height of -1. The scale will be fixed, and that may not look great with a pre-determined size. -158: file bond_highlights_8.svg gave hash 1272407071U not the expected 2956924065U -158: file test_github5947.svg gave hash 737562322U not the expected 3122633523U -158: file test_github6112.svg gave hash 3291975047U not the expected 3278777629U -158: file test_github6200_1.svg gave hash 1975293465U not the expected 1044179149U -158: file github6336_1.png gave hash 1930712448U not the expected 2958833204U -158: file test_github6397_2.svg gave hash 2405824082U not the expected 3422233570U -158: file test_github6397_3.svg gave hash 759740391U not the expected 3320683230U -158: file test_github6397_4.svg gave hash 2454933776U not the expected 2960192928U -158: file test_github6397_5.svg gave hash 1843492326U not the expected 1245534660U -158: file github6504_1.svg gave hash 3649936662U not the expected 1429448598U -158: file github6504_2.svg gave hash 106020287U not the expected 2871662880U -158: file github6569_1.svg gave hash 1698514747U not the expected 116573839U -158: file github6569_2.svg gave hash 2778768241U not the expected 2367779037U -158: file AtropCanon1.svg gave hash 818325437U not the expected 526339583U -158: file AtropManyChiralsEnhanced.svg gave hash 292902747U not the expected 348414093U -158: file testGithub6968.svg gave hash 940962291U not the expected 1554428830U -158: file testWedgeNonSingleBonds-1.svg gave hash 2116685919U not the expected 865601717U -158: file testWedgeNonSingleBonds-2.svg gave hash 1174395532U not the expected 2960559495U -158: file testWedgeNonSingleBonds-3.svg gave hash 2542970771U not the expected 1428196589U -158: file testWedgeNonSingleBonds-4.svg gave hash 700876833U not the expected 3897680387U -158: file testWedgeNonSingleBonds-5.svg gave hash 2012191155U not the expected 2183530217U -158: file testWedgeNonSingleBonds-6.svg gave hash 2517061935U not the expected 238313010U -158: file testWedgeNonSingleBonds-7.svg gave hash 157069219U not the expected 3641456570U -158: file testWedgeNonSingleBonds-8.svg gave hash 3431784338U not the expected 3209701539U -158: file testWedgingShouldBeOnSingleBond.svg gave hash 2637422009U not the expected 1002741488U -158: file testHighlightHeteroAtoms_1.svg gave hash 4006401146U not the expected 1769258632U -158: file testHighlightHeteroAtoms_2.svg gave hash 1248188292U not the expected 893937335U -158: file testGithub_7739_1.svg gave hash 233164329U not the expected 52079325U -158: file testGithub_7739_3.svg gave hash 1653424667U not the expected 1126644226U -158: file testGithub_7739_4.svg gave hash 3214282623U not the expected 9844878U -161: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds -161: Time elapsed 0.000 seconds -161: -161: test32() -161: MCS: [#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#6]=[#6]-[#6](-[#7]-[#6]1:[#6]:[#6](-[#16](-[#7]2-[#6]-[#6]-[#8]-[#6]-[#6]-2)(=[#8])=[#8]):[#6]:[#6]:[#6]:1-[#7](-[#6]-[#6])-[#6]-[#6])=[#8] 31 atoms, 33 bonds -161: Time elapsed 0.063 seconds -161: -161: test190() -161: MCS: [#6]1:[#6]:[#6]2:[#8]:[#6](:[#7]:[#6]:2:[#6]:[#6]:1)-[#6]1:[#6]:[#6](-[#7]-[#6](=[#8])-[#6]):[#6]:[#6]:[#6]:1 19 atoms, 21 bonds -161: Time elapsed 0.009 seconds -161: -161: test3() -161: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6]-[#6](=[#8])-[#7]-[#6]-[#6]-[#6]-[#6] 14 atoms, 14 bonds -161: Time elapsed 0.012 seconds -161: -161: testSimpleFast() -161: MCS: [#6]-[#8]-[#6]-[#6]1:[#6]:[#7]:[#6]:[#6](:[#6]:1):[#7]:[#6]1:[#6]:[#6]:[#6]:[#6](:[#6]:1)-[#8]-[#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#17] 24 atoms, 26 bonds -161: Time elapsed 0.091 seconds -161: -161: testSimple() -161: MCS: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -161: Time elapsed 0.149 seconds -161: MCS MatchFusedRings: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -161: Time elapsed 0.279 seconds -161: MCS MatchFusedRingsStrict: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -161: Time elapsed 0.225 seconds -161: -161: testSegFault() -161: MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -161: Time elapsed 0.013 seconds -161: MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -161: Time elapsed 0.027 seconds -161: MCS MatchFusedRingsStrict: [#6;r6,!R1]1:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@1 6 atoms, 6 bonds -161: Time elapsed 0.023 seconds -161: -161: testThreshold() -161: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -161: Time elapsed 0.000 seconds -161: -161: testRing1() -161: MCS: [#6]-&!@[#8]-&!@[#6]-&!@[#6]1:&@[#6]:&@[#7]:&@[#6]:&@[#6]2:&@[#6]:&@1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#7]:&@2 16 atoms, 17 bonds -161: Time elapsed 0.676 seconds -161: MCS MatchFusedRings: [#6]-&!@[#8]-&!@[#6]-&!@[#6]1:&@[#6]:&@[#7]:&@[#6]:&@[#6]2:&@[#6]:&@1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#7]:&@2 16 atoms, 17 bonds -161: Time elapsed 0.769 seconds -161: MCS MatchFusedRingsStrict: [#6;r6,!R1]1:&@[#6;r6,!R1]:&@[#7;r6,!R1]:&@[#6;r6,!R1](:&@[#6]:&@[#6]:&@1)-&!@[#6](=&!@[#8])-&!@[#8]-&!@[#6](-&!@[#6])-&!@[#6] 12 atoms, 12 bonds -161: Time elapsed 0.815 seconds -161: -161: testAtomCompareIsotopes() -161: MCS: [0*]-[0*]-[13*] 3 atoms, 2 bonds -161: Time elapsed 0.000 seconds -161: -161: testAtomCompareAnyAtom() -161: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds -161: Time elapsed 0.000 seconds -161: -161: testAtomCompareAnyAtom() -161: MCS: [#6]1-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:1=,-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds -161: Time elapsed 0.000 seconds -161: -161: testAtomCompareAnyAtom() -161: MCS: [#1]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 8 atoms, 8 bonds -161: Time elapsed 0.000 seconds -161: -161: testAtomCompareAnyAtom() -161: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 7 atoms, 7 bonds -161: Time elapsed 0.000 seconds -161: -161: testJnk1LigandsDistance() -161: MCS: [#6]-[#6]-[#8]-[#6]1:[#6](:[#6](:[#6]:[#6](:[#7]:1)-[#7]-[#6](=[#8])-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1)-[#7])-[#6]#[#7] CCOc1nc(NC(=O)Cc2ccccc2)cc(N)c1C#N 22 atoms, 23 bonds -161: Time elapsed 0.005 seconds -161: MCS: [#6]-[#6]-[#8]-[#6]1:[#6](:[#6](:[#6]:[#6](:[#7]:1)-[#7]-[#6](=[#8])-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6](:[#6]:1)-[#6,#8])-[#7])-[#6]#[#7] *c1cccc(CC(=O)Nc2cc(N)c(C#N)c(OCC)n2)c1 23 atoms, 24 bonds -158: [02:23:07] -158: -158: **** -158: Pre-condition Violation -158: -158: Violation occurred on line 206 in file ./Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.cpp -158: Failed Expression: atomIdx < atCds_.size() && atomIdx < atomLabels_.size() -158: ---------- -158: Stacktrace: -158: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -158: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -158: 2# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::calcSymbolEllipse(unsigned int, RDGeom::Point2D&, double&, double&) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -158: 3# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::makeAtomHighlights(std::vector >, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -158: 4# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::extractMCHighlights() in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -158: 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -158: 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -158: 7# RDKit::MolDraw2D::drawMoleculeWithHighlights(RDKit::ROMol const&, std::__cxx11::basic_string, std::allocator > const&, std::map >, std::less, std::allocator > > > > const&, std::map >, std::less, std::allocator > > > > const&, std::map, std::allocator > > const&, std::map, std::allocator > > const&, int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -158: 8# 0x0000AAAAB8B04468 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 9# 0x0000AAAAB8BCA1AC in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 10# 0x0000AAAAB8BCAB60 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 11# 0x0000AAAAB8BCAF94 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 12# 0x0000AAAAB8B9F998 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 13# 0x0000AAAAB8B9FEE4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 14# 0x0000AAAAB8AFDB10 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 15# 0x0000FFFFB142229C in /lib/aarch64-linux-gnu/libc.so.6 -158: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -158: 17# 0x0000AAAAB8AFDBF0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: ---------- -158: **** -158: -158: [02:23:07] -158: -158: **** -158: Range Error -158: idx -158: Violation occurred on line 329 in file ./Code/GraphMol/ROMol.cpp -158: Failed Expression: 2 < 0 -158: ---------- -158: Stacktrace: -158: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -158: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -158: 2# RDKit::ROMol::getBondWithIdx(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -158: 3# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::makeBondHighlights(std::vector >, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -158: 4# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::extractMCHighlights() in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -158: 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -158: 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -158: 7# RDKit::MolDraw2D::drawMoleculeWithHighlights(RDKit::ROMol const&, std::__cxx11::basic_string, std::allocator > const&, std::map >, std::less, std::allocator > > > > const&, std::map >, std::less, std::allocator > > > > const&, std::map, std::allocator > > const&, std::map, std::allocator > > const&, int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -158: 8# 0x0000AAAAB8B03EAC in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 9# 0x0000AAAAB8BCA1AC in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 10# 0x0000AAAAB8BCAB60 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 11# 0x0000AAAAB8BCAF94 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 12# 0x0000AAAAB8B9F998 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 13# 0x0000AAAAB8B9FEE4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 14# 0x0000AAAAB8AFDB10 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 15# 0x0000FFFFB142229C in /lib/aarch64-linux-gnu/libc.so.6 -158: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -158: 17# 0x0000AAAAB8AFDBF0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: ---------- -158: **** -158: -158: [02:23:07] -158: -158: **** -158: Range Error -158: idx -158: Violation occurred on line 329 in file ./Code/GraphMol/ROMol.cpp -158: Failed Expression: 0 < 0 -158: ---------- -158: Stacktrace: -158: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -158: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -158: 2# RDKit::ROMol::getBondWithIdx(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -158: 3# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::makeBondHighlights(std::vector >, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -158: 4# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::extractMCHighlights() in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -158: 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -158: 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -158: 7# RDKit::MolDraw2D::drawMoleculeWithHighlights(RDKit::ROMol const&, std::__cxx11::basic_string, std::allocator > const&, std::map >, std::less, std::allocator > > > > const&, std::map >, std::less, std::allocator > > > > const&, std::map, std::allocator > > const&, std::map, std::allocator > > const&, int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -158: 8# 0x0000AAAAB8B04514 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 9# 0x0000AAAAB8BCA1AC in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 10# 0x0000AAAAB8BCAB60 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 11# 0x0000AAAAB8BCAF94 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 12# 0x0000AAAAB8B9F998 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 13# 0x0000AAAAB8B9FEE4 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 14# 0x0000AAAAB8AFDB10 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: 15# 0x0000FFFFB142229C in /lib/aarch64-linux-gnu/libc.so.6 -158: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -158: 17# 0x0000AAAAB8AFDBF0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -158: ---------- -158: **** -158: -158: =============================================================================== -158: All tests passed (6801 assertions in 105 test cases) -158: -156/230 Test #158: moldraw2DTestCatch ..................... Passed 3.53 sec +156/230 Test #162: pyFMCS ................................. Passed 7.43 sec test 168 Start 168: testRascalMCES 168: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/testRascalMCES 168: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES 168: Test timeout computed to be: 1500 -161: Time elapsed 0.001 seconds -161: -161: test18() -161: Query +MAP [CH3:0][c:1]1[n:2][c:3]([CH2:4][N:5]([CH:6]([CH3:7])[c:8]2[n:9][cH:10][cH:11][cH:12][cH:13]2)[CH2:14][CH2:15][CH2:16][CH2:17][NH2:18])[cH:19][cH:20][cH:21]1 -161: MCS: [#6](:[#7]:[#6]-[#6]-[#7](-[#6](-[#6])-[#6]1:[#7]:[#6]:[#6]:[#6]:[#6]:1)-[#6]-[#6]-[#6]-[#6]-[#7]):[#6]:[#6]:[#6] 21 atoms, 21 bonds -161: Time elapsed 0.005 seconds -161: -161: test504() -161: Query +MAP [CH2:0]([CH2:1][CH2:2][NH:3][C:4]([CH:5]1[CH2:6][CH:7]1[c:8]1[c:9][c:10]([Cl:11])[c:12]([Cl:13])[cH:14][c:15]1)=[O:16])[CH2:17][CH2:18][N:19]1[CH2:20][CH2:21][CH:22]([NH:23][C:24]([NH:25][c:26]2[cH:27][cH:28][c:29]([Cl:30])[cH:31][cH:32]2)=[O:33])[CH2:34]1 -161: MCS: [#6](-[#6]-[#6]-[#7]-[#6](-[#6]1-[#6]-[#6]-1-[#6]1:[#6]:[#6](-[#17]):[#6](:[#6]:[#6]:1)-[#17])=[#8])-[#6]-[#6]-[#7](-[#6]-[#6]-[#6]-[#7]-[#6](-[#7]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1)=[#8])-[#6] 34 atoms, 36 bonds -161: Time elapsed 0.149 seconds -161: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds -161: Time elapsed 0.001 seconds -161: MCS: [#6]1-[#6]-[#7]-[#6](-[#6]-[#7]-1-[#6]1:[#6](:[#6]:[#6]2:[#6](:[#6](:[#6]:[#7](-[#6]3-[#6]-[#6]-3):[#6]:2:[#6]:1)-[#6](=[#8])-[#8])=[#8])-[#9])-[#6] 25 atoms, 28 bonds -161: Time elapsed 0.038 seconds -161: Query Cc1c(F)c(N2CCNC(C)C2)cc2c1c(=O)c(C(=O)O)cn2C1CC1 26(26) atoms, 29(28) bonds -161: 1 Seeds:1 MCS 25 atoms, 28 bonds for 0.0008 seconds. bond[0]=6 -161: STATISTICS: -161: Total Growing Steps = 1, MCS found on 1 step, for 0.0008 seconds -161: Initial Seeds = 1, Mismatched 0 -161: Inspected Seeds = 2 -161: Rejected by BestSize = 0 -161: IndividualBondExcluded = 0 -161: MatchCheck Seeds = 2 -161: MatchCalls = 2 -161: MatchFound = 1 -161: fastMatchCalls = 1 -161: fastMatchFound = 0 -161: slowMatchCalls = 2 -161: slowMatchFound = 1 -161: DupCacheFound = 0 0 matched, 0 mismatched -161: HashCache size = 1 keys -161: HashCache size = 1 entries -161: FindHashInCache = 2 -161: HashFoundInCache= 0 -161: ExactMatchCalls = 0 -161: ExactMatchFound = 0 -161: Time elapsed 0.001 seconds -161: query=OCCl SubstructMatch(useChirality=false) res =1 size=3 -161: query=OCCl SubstructMatch(useChirality=true ) res =1 size=3 -161: test target = O[C@H](F)CCl query = C(F)C useChirality = 0 -161: res sub = 1 size=3 -161: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds -161: test target = O[C@H](F)CCl query = C(F)C useChirality = 1 -161: res sub = 1 size=3 -161: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds -161: test target = CC[C@H](F)Cl query = CCC useChirality = 0 -161: res sub = 1 size=3 -161: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -161: test target = CC[C@H](F)Cl query = CCC useChirality = 1 -161: res sub = 1 size=3 -161: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -161: test target = CCC(F)Cl query = CC useChirality = 0 -161: res sub = 1 size=2 -161: MCS: [#6]-[#6] 2 atoms, 1 bonds -161: test target = CCC(F)Cl query = CC useChirality = 1 -161: res sub = 1 size=2 -161: MCS: [#6]-[#6] 2 atoms, 1 bonds -161: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 0 -161: res sub = 1 size=4 -161: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -161: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 1 -161: res sub = 1 size=4 -161: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -161: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 0 -161: res sub = 1 size=4 -161: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -161: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 1 -161: res sub = 1 size=4 -161: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -161: test target = O[C@H](F)CCl query = CC(F)C useChirality = 0 -161: res sub = 0 size=0 -161: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds -161: test target = O[C@H](F)CCl query = CC(F)C useChirality = 1 -161: res sub = 0 size=0 -161: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds -161: test target = O[C@H](F)CCl query = OC(F)C useChirality = 0 -161: res sub = 1 size=4 -161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -161: test target = O[C@H](F)CCl query = OC(F)C useChirality = 1 -161: res sub = 1 size=4 -161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -161: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 0 -161: res sub = 1 size=4 -161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -161: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 1 -161: res sub = 1 size=4 -161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -161: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 0 -161: res sub = 1 size=4 -161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -161: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 1 -161: res sub = 0 size=0 -161: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -161: test target = OC(F)CCl query = OC(F)C useChirality = 0 -161: res sub = 1 size=4 -161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -161: test target = OC(F)CCl query = OC(F)C useChirality = 1 -161: res sub = 1 size=4 -161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -161: test target = OC(F)CCl query = O[C@H](F)C useChirality = 0 -161: res sub = 1 size=4 -161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -161: test target = OC(F)CCl query = O[C@H](F)C useChirality = 1 -161: res sub = 0 size=0 -161: MCS: [#9] 1 atoms, 0 bonds -161: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 0 -161: res sub = 1 size=4 -161: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -161: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 1 -161: res sub = 0 size=0 -161: MCS: [#9] 1 atoms, 0 bonds -161: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 0 -161: res sub = 1 size=3 -161: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -161: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 1 -161: res sub = 1 size=3 -161: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -161: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 0 -161: res sub = 1 size=3 -161: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -161: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 1 -161: res sub = 1 size=3 -161: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -161: -161: 0. <<<<<<<<< actual MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds >>>>>>> -161: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 0 -161: res sub = 1 size=3 -161: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -161: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 1 -161: res sub = 1 size=3 -161: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -161: done 167: ......... 167: ---------------------------------------------------------------------- -167: Ran 9 tests in 2.536s +167: Ran 9 tests in 1.946s 167: 167: OK -157/230 Test #167: pyMMPA ................................. Passed 2.88 sec +157/230 Test #167: pyMMPA ................................. Passed 2.59 sec test 169 Start 169: testRascalCluster 169: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/testRascalCluster 169: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES 169: Test timeout computed to be: 1500 -162: ........................................[02:23:09] The provided InitialSeed is not an MCS and will be ignored -162: [02:23:09] The provided InitialSeed is not an MCS and will be ignored -162: [02:23:09] The provided InitialSeed is not an MCS and will be ignored -162: .[02:23:09] The provided InitialSeed is not an MCS and will be ignored -162: [02:23:09] The provided InitialSeed is not an MCS and will be ignored -162: [02:23:09] The provided InitialSeed is not an MCS and will be ignored -162: .[02:23:09] The provided InitialSeed is not an MCS and will be ignored -162: [02:23:09] The provided InitialSeed is not an MCS and will be ignored -162: [02:23:09] The provided InitialSeed is not an MCS and will be ignored -162: .[02:23:09] The provided InitialSeed is not an MCS and will be ignored -162: [02:23:09] The provided InitialSeed is not an MCS and will be ignored -162: [02:23:09] The provided InitialSeed is not an MCS and will be ignored -162: ................. -162: ---------------------------------------------------------------------- -162: Ran 60 tests in 5.128s -162: -162: OK -158/230 Test #162: pyFMCS ................................. Passed 5.90 sec -test 170 - Start 170: pyRascalMCES - -170: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/Wrap/testRascalMCES.py" -170: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/Wrap -170: Test timeout computed to be: 1500 -161: [02:23:10] The provided InitialSeed is not an MCS and will be ignored -170: ..........Too many matching bond pairs (1032) so can't continue. -170: ... -170: ---------------------------------------------------------------------- -170: Ran 13 tests in 2.691s -170: -170: OK -150: .............[02:23:14] Molecule does not have explicit Hs. Consider calling AddHs() -159/230 Test #170: pyRascalMCES ........................... Passed 3.76 sec -test 171 - Start 171: testCIPLabeler - -171: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/testCIPLabeler -171: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler -171: Test timeout computed to be: 1500 -171: Randomness seeded to: 1769317468 -171: [02:23:14] non kekulizable aromatic bond being treated as bond order 1 -171: [02:23:14] non kekulizable aromatic bond being treated as bond order 1 -171: [02:23:14] non kekulizable aromatic bond being treated as bond order 1 -171: [02:23:14] non kekulizable aromatic bond being treated as bond order 1 -171: [02:23:14] non kekulizable aromatic bond being treated as bond order 1 -171: [02:23:14] non kekulizable aromatic bond being treated as bond order 1 -150: [02:23:14] Molecule does not have explicit Hs. Consider calling AddHs() -150: [02:23:14] Molecule does not have explicit Hs. Consider calling AddHs() -150: [02:23:14] Molecule does not have explicit Hs. Consider calling AddHs() -171: [02:23:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -171: [02:23:14] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -150: [02:23:14] Molecule does not have explicit Hs. Consider calling AddHs() -171: =============================================================================== -171: All tests passed (6572 assertions in 18 test cases) -171: -160/230 Test #171: testCIPLabeler ......................... Passed 0.34 sec -test 172 - Start 172: pyCIPLabelsWrapTest - -172: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelWrapTest.py" -172: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap -172: Test timeout computed to be: 1500 -150: [02:23:14] Molecule does not have explicit Hs. Consider calling AddHs() -150: [02:23:14] Molecule does not have explicit Hs. Consider calling AddHs() -150: [02:23:14] Molecule does not have explicit Hs. Consider calling AddHs() -150: [02:23:14] Molecule does not have explicit Hs. Consider calling AddHs() -150: [02:23:14] Molecule does not have explicit Hs. Consider calling AddHs() -150: [02:23:14] Molecule does not have explicit Hs. Consider calling AddHs() -169: Randomness seeded to: 558098078 -169: /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/data/chembl_1907596.smi -172: .... -172: ---------------------------------------------------------------------- -172: Ran 4 tests in 0.018s -172: -172: OK -161/230 Test #172: pyCIPLabelsWrapTest .................... Passed 0.71 sec -test 173 - Start 173: pyCIPLabelsValidation - -173: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelsValidation.py" -173: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap -173: Test timeout computed to be: 1500 157: Done 157: ----------------- Test Github #781: Rendering single-atom molecules 157: Done @@ -31399,18 +31353,95 @@ 157: Done 157: ----------------- Test AND queries 157: Done -162/230 Test #157: moldraw2DTest1 ......................... Passed 13.37 sec +158/230 Test #157: moldraw2DTest1 ......................... Passed 13.71 sec +test 170 + Start 170: pyRascalMCES + +170: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/Wrap/testRascalMCES.py" +170: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/Wrap +170: Test timeout computed to be: 1500 +170: ..........Too many matching bond pairs (1032) so can't continue. +170: ... +170: ---------------------------------------------------------------------- +170: Ran 13 tests in 3.107s +170: +170: OK +159/230 Test #170: pyRascalMCES ........................... Passed 4.52 sec +test 171 + Start 171: testCIPLabeler + +171: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/testCIPLabeler +171: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler +171: Test timeout computed to be: 1500 +171: Randomness seeded to: 2045164571 +171: [23:10:21] non kekulizable aromatic bond being treated as bond order 1 +171: [23:10:21] non kekulizable aromatic bond being treated as bond order 1 +171: [23:10:21] non kekulizable aromatic bond being treated as bond order 1 +171: [23:10:21] non kekulizable aromatic bond being treated as bond order 1 +171: [23:10:21] non kekulizable aromatic bond being treated as bond order 1 +171: [23:10:21] non kekulizable aromatic bond being treated as bond order 1 +171: [23:10:21] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +171: [23:10:21] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +171: =============================================================================== +171: All tests passed (6572 assertions in 18 test cases) +171: +160/230 Test #171: testCIPLabeler ......................... Passed 0.50 sec +test 172 + Start 172: pyCIPLabelsWrapTest + +172: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelWrapTest.py" +172: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap +172: Test timeout computed to be: 1500 +172: .... +172: ---------------------------------------------------------------------- +172: Ran 4 tests in 0.038s +172: +172: OK +161/230 Test #172: pyCIPLabelsWrapTest .................... Passed 1.14 sec +test 173 + Start 173: pyCIPLabelsValidation + +173: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelsValidation.py" +173: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap +173: Test timeout computed to be: 1500 +168: Randomness seeded to: 3266054135 +168: Timed out after 11 seconds. +150: .............[23:10:24] Molecule does not have explicit Hs. Consider calling AddHs() +150: [23:10:24] Molecule does not have explicit Hs. Consider calling AddHs() +150: [23:10:24] Molecule does not have explicit Hs. Consider calling AddHs() +150: [23:10:24] Molecule does not have explicit Hs. Consider calling AddHs() +150: [23:10:24] Molecule does not have explicit Hs. Consider calling AddHs() +150: [23:10:24] Molecule does not have explicit Hs. Consider calling AddHs() +150: [23:10:25] Molecule does not have explicit Hs. Consider calling AddHs() +150: [23:10:25] Molecule does not have explicit Hs. Consider calling AddHs() +150: [23:10:25] Molecule does not have explicit Hs. Consider calling AddHs() +150: [23:10:25] Molecule does not have explicit Hs. Consider calling AddHs() +150: [23:10:25] Molecule does not have explicit Hs. Consider calling AddHs() +169: Randomness seeded to: 1485103413 +169: /build/reproducible-path/rdkit-202409.2/Code/GraphMol/RascalMCES/data/chembl_1907596.smi +150: ...[23:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +150: [23:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +150: [23:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +150: [23:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +150: [23:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +150: ... +150: ---------------------------------------------------------------------- +150: Ran 19 tests in 29.073s +150: +150: OK +150: Testing MolAlign Wrappers +162/230 Test #150: pyMolAlign ............................. Passed 30.66 sec test 174 Start 174: deprotectTest 174: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect/deprotectTest 174: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect 174: Test timeout computed to be: 1500 -174: Randomness seeded to: 519068935 +174: Randomness seeded to: 3468204643 174: =============================================================================== 174: All tests passed (111 assertions in 3 test cases) 174: -163/230 Test #174: deprotectTest .......................... Passed 0.07 sec +163/230 Test #174: deprotectTest .......................... Passed 0.19 sec test 175 Start 175: pyDeprotect @@ -31419,7 +31450,7 @@ 175: Test timeout computed to be: 1500 175: ..... 175: ---------------------------------------------------------------------- -175: Ran 5 tests in 0.022s +175: Ran 5 tests in 0.088s 175: 175: OK 175: Testing tert-butyldimethylsilyl @@ -31472,7 +31503,7 @@ 175: Testing acetamide 175: Testing carbobenzyloxy 175: Testing Acetal/Ketal -164/230 Test #175: pyDeprotect ............................ Passed 0.27 sec +164/230 Test #175: pyDeprotect ............................ Passed 1.15 sec test 176 Start 176: testReducedGraphs @@ -31497,7 +31528,7 @@ 176: 176: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] 176: -165/230 Test #176: testReducedGraphs ...................... Passed 0.02 sec +165/230 Test #176: testReducedGraphs ...................... Passed 0.11 sec test 177 Start 177: pyReducedGraphs @@ -31506,485 +31537,512 @@ 177: Test timeout computed to be: 1500 177: ..... 177: ---------------------------------------------------------------------- -177: Ran 5 tests in 0.021s +177: Ran 5 tests in 0.054s 177: 177: OK -166/230 Test #177: pyReducedGraphs ........................ Passed 0.36 sec +166/230 Test #177: pyReducedGraphs ........................ Passed 1.31 sec test 178 Start 178: trajectoryTest 178: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory/trajectoryTest 178: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory 178: Test timeout computed to be: 1500 -167/230 Test #178: trajectoryTest ......................... Passed 0.56 sec +167/230 Test #178: trajectoryTest ......................... Passed 0.86 sec test 179 Start 179: substructLibraryTest 179: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryTest 179: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary 179: Test timeout computed to be: 1500 -179: [02:23:18] ------------------------------------- -179: [02:23:18] Test1 -168: Randomness seeded to: 1957238971 -168: Timed out after 11 seconds. -179: [02:23:19] done -179: [02:23:19] ------------------------------------- -179: [02:23:19] Test2 -150: ...[02:23:19] Molecule does not have explicit Hs. Consider calling AddHs() -150: [02:23:19] Molecule does not have explicit Hs. Consider calling AddHs() -150: [02:23:19] Molecule does not have explicit Hs. Consider calling AddHs() -150: [02:23:19] Molecule does not have explicit Hs. Consider calling AddHs() -150: [02:23:19] Molecule does not have explicit Hs. Consider calling AddHs() -150: ... -150: ---------------------------------------------------------------------- -150: Ran 19 tests in 19.225s -150: -150: OK -150: Testing MolAlign Wrappers -168/230 Test #150: pyMolAlign ............................. Passed 20.02 sec +179: [23:10:34] ------------------------------------- +179: [23:10:34] Test1 +179: [23:10:34] done +179: [23:10:34] ------------------------------------- +179: [23:10:34] Test2 +179: [23:10:35] done +179: [23:10:35] ------------------------------------- +179: [23:10:35] Test3 (stereo options) +179: [23:10:35] Done (stereo options) +179: [23:10:35] ------------------------------------- +179: [23:10:35] Test4 (trusted smiles) +179: [23:10:35] Done (trusted smiles) +179: [23:10:35] ------------------------------------- +179: [23:10:35] Testing C++ docs +179: [23:10:35] Done (C++ doc tests) +179: [23:10:35] ------------------------------------- +179: [23:10:35] Testing C++ ring query: PatternHolder +179: [23:10:35] Done (C++ ring query tests) +179: [23:10:35] ------------------------------------- +179: [23:10:35] Testing C++ ring query: TautomerPatternHolder +179: [23:10:35] Done (C++ ring query tests) +179: [23:10:35] ------------------------------------- +179: [23:10:35] Add Patterns +161: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds +161: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds +161: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds +161: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds +161: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds +161: MCS MatchStereo true : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds +161: TOTAL Time elapsed 32.85 seconds +168/230 Test #161: testFMCS ............................... Passed 33.04 sec test 180 Start 180: substructLibraryCatchTest 180: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryCatchTest 180: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary 180: Test timeout computed to be: 1500 -179: [02:23:19] done -179: [02:23:19] ------------------------------------- -179: [02:23:19] Test3 (stereo options) -179: [02:23:19] Done (stereo options) -179: [02:23:19] ------------------------------------- -179: [02:23:19] Test4 (trusted smiles) -179: [02:23:19] Done (trusted smiles) -179: [02:23:19] ------------------------------------- -179: [02:23:19] Testing C++ docs -179: [02:23:19] Done (C++ doc tests) -179: [02:23:19] ------------------------------------- -179: [02:23:19] Testing C++ ring query: PatternHolder -179: [02:23:19] Done (C++ ring query tests) -179: [02:23:19] ------------------------------------- -179: [02:23:19] Testing C++ ring query: TautomerPatternHolder -179: [02:23:19] Done (C++ ring query tests) -179: [02:23:19] ------------------------------------- -179: [02:23:19] Add Patterns -180: Randomness seeded to: 2642705569 +148: --------------------------------- +148: test O3A multithreading bug +148: +148: --------------------------------- +148: testCrippenO3A multithreading +148: +148: generating reference data +146: .........[23:10:39] Molecule does not have explicit Hs. Consider calling AddHs() +146: .[23:10:39] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:10:39] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:10:39] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:10:39] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:10:39] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:10:39] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:10:39] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:10:39] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:10:39] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:10:39] Molecule does not have explicit Hs. Consider calling AddHs() +146: .[23:10:39] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:10:39] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:10:39] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:10:39] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:10:39] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:10:39] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:10:39] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:10:39] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:10:39] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:10:39] Molecule does not have explicit Hs. Consider calling AddHs() +180: Randomness seeded to: 1596107155 180: =============================================================================== 180: All tests passed (171 assertions in 5 test cases) 180: -169/230 Test #180: substructLibraryCatchTest .............. Passed 1.92 sec +169/230 Test #180: substructLibraryCatchTest .............. Passed 2.22 sec test 181 Start 181: pySubstructLibrary 181: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/SubstructLibrary/Wrap/rough_test.py" 181: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap 181: Test timeout computed to be: 1500 -179: [02:23:26] ------------------------------------- -179: [02:23:26] testing PatternHolder -179: [02:23:27] ------------------------------------- -179: [02:23:27] testing TautomerPatternHolder -179: [02:23:27] ------------------------------------- -179: [02:23:27] testSegFaultInHolder -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[02:23:27] [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'SMILES Parse Error: -179: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf +148: processing +148: launch :0 +148: launch :1 +148: launch :2 +148: launch :3 +179: [23:10:42] ------------------------------------- +179: [23:10:42] testing PatternHolder +179: [23:10:42] ------------------------------------- +179: [23:10:42] testing TautomerPatternHolder +179: [23:10:43] ------------------------------------- +179: [23:10:43] testSegFaultInHolder +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: syntax error[23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf[23:10:43] SMILES' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: [23:10:43] Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: dsafsdf' +179: [23:10:43] [23:10:43] syntax error while parsing: dsafsdf 179: SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] [02:23:27] [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 179: SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: syntax error[23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf[23:10:43] while parsing: dsafsdf 179: SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] SMILES Parse Error: syntax error while parsing: dsafsdf -179: [02:23:27] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -179: [02:23:27] ------------------------------------- -179: [02:23:27] Results do not depend on numThreads +179: [23:10:43] SMILES Parse Error: syntax error[23:10:43] [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: ' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] SMILES Parse Error: syntax error while parsing: dsafsdf +179: [23:10:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +179: [23:10:43] ------------------------------------- +179: [23:10:43] Results do not depend on numThreads 173: VS001: PASSED 173: VS002: PASSED 173: VS003: PASSED @@ -32287,139 +32345,136 @@ 173: VS300: PASSED 173: Check finished: 0 molecules failed. 173: Failed: -170/230 Test #173: pyCIPLabelsValidation .................. Passed 12.68 sec +170/230 Test #173: pyCIPLabelsValidation .................. Passed 21.39 sec test 182 Start 182: testRGroupDecomp 182: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecomp 182: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition 182: Test timeout computed to be: 1500 -182: [02:23:28] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters -182: [02:23:28] WARNING: not removing hydrogen atom with dummy atom neighbors -161: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds -161: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds -161: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds -161: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds -161: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds -161: MCS MatchStereo true : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds -161: TOTAL Time elapsed 24.88 seconds -171/230 Test #161: testFMCS ............................... Passed 24.96 sec +182: [23:10:45] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters +182: [23:10:45] WARNING: not removing hydrogen atom with dummy atom neighbors +146: ... +146: ---------------------------------------------------------------------- +146: Ran 22 tests in 48.653s +146: +146: OK +171/230 Test #146: pyDistGeomHelpers ...................... Passed 49.63 sec test 183 Start 183: testRGroupDecompInternals 183: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecompInternals 183: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition 183: Test timeout computed to be: 1500 -183: [02:23:29] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [02:23:29] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [02:23:29] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [02:23:29] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [02:23:29] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [02:23:29] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [02:23:29] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [02:23:29] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [02:23:29] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [02:23:29] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [02:23:29] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [02:23:29] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [02:23:29] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [02:23:29] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [02:23:29] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [02:23:29] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [02:23:29] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [02:23:29] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [02:23:29] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [02:23:29] WARNING: not removing hydrogen atom with dummy atom neighbors -183: [02:23:29] WARNING: not removing hydrogen atom with dummy atom neighbors -172/230 Test #183: testRGroupDecompInternals .............. Passed 0.06 sec +183: [23:10:48] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [23:10:48] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [23:10:48] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [23:10:48] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [23:10:48] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [23:10:48] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [23:10:48] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [23:10:48] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [23:10:48] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [23:10:48] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [23:10:48] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [23:10:48] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [23:10:48] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [23:10:48] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [23:10:48] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [23:10:48] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [23:10:48] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [23:10:48] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [23:10:48] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [23:10:48] WARNING: not removing hydrogen atom with dummy atom neighbors +183: [23:10:48] WARNING: not removing hydrogen atom with dummy atom neighbors +172/230 Test #183: testRGroupDecompInternals .............. Passed 0.10 sec test 184 Start 184: rgroupCatchTests 184: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/rgroupCatchTests 184: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition 184: Test timeout computed to be: 1500 -184: Randomness seeded to: 1021852412 +184: Randomness seeded to: 3565386707 184: =============================================================================== 184: All tests passed (1475 assertions in 14 test cases) 184: -173/230 Test #184: rgroupCatchTests ....................... Passed 0.64 sec +173/230 Test #184: rgroupCatchTests ....................... Passed 0.61 sec test 185 Start 185: pyRGroupDecomposition 185: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/RGroupDecomposition/Wrap/test_rgroups.py" 185: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap 185: Test timeout computed to be: 1500 -179: [02:23:32] ------------------------------------- -179: [02:23:32] Results do not depend on numThreads (all same) -185: .................... -185: ---------------------------------------------------------------------- -185: Ran 20 tests in 1.371s -185: -185: OK 182: iterative -174/230 Test #185: pyRGroupDecomposition .................. Passed 2.19 sec +179: [23:10:50] ------------------------------------- +179: [23:10:50] Results do not depend on numThreads (all same) +179: [23:10:50] ------------------------------------- +179: [23:10:50] testTautomerQueries +179: [23:10:50] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... +179: [23:10:50] ------------------------------------- +179: [23:10:50] github3881 recursive smarts with rings +174/230 Test #179: substructLibraryTest ................... Passed 16.83 sec test 186 Start 186: molInterchangeTest1 186: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeTest1 186: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange 186: Test timeout computed to be: 1500 -186: [02:23:32] test1: basics -186: [02:23:32] done -186: [02:23:32] test2: basic writing +186: [23:10:50] test1: basics +182: bulk +186: [23:10:50] done +186: [23:10:50] test2: basic writing 186: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"mol1 name","atoms":[{"impHs":3},{"impHs":3}],"bonds":[{"atoms":[0,1]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.2","cipRanks":[0,0]}]}]} 186: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"z":9},{"stereo":"cw"},{"z":17},{"z":8,"impHs":1},{"impHs":3}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[1,3]},{"atoms":[1,4]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.2","cipRanks":[3,1,4,2,0],"cipCodes":[[1,"S"]]}]}]} 186: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1}],"bonds":[{"bo":2,"atoms":[0,1]},{"atoms":[1,2]},{"bo":2,"atoms":[2,3]},{"atoms":[3,4]},{"bo":2,"atoms":[4,5]},{"atoms":[5,0]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.2","aromaticAtoms":[0,1,2,3,4,5],"aromaticBonds":[0,1,2,3,4,5],"cipRanks":[0,0,0,0,0,0],"atomRings":[[0,5,4,3,2,1]]}]}]} 186: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":3},{"impHs":2},{},{},{"z":7,"impHs":2},{"impHs":1},{},{"impHs":3},{"z":7},{"impHs":1}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"bo":2,"atoms":[2,3]},{"atoms":[3,4]},{"atoms":[3,5]},{"bo":2,"atoms":[5,6]},{"atoms":[6,7]},{"atoms":[6,8]},{"bo":2,"atoms":[8,9]},{"atoms":[9,2]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.2","aromaticAtoms":[2,3,5,6,8,9],"aromaticBonds":[2,4,5,7,8,9],"cipRanks":[0,2,4,5,8,3,7,1,9,6],"atomRings":[[2,9,8,6,5,3]]}]}]} -186: [02:23:32] done -186: [02:23:32] test3: writing conformers +186: [23:10:50] done +186: [23:10:50] test3: writing conformers 186: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"example 2","atoms":[{"z":8},{"stereo":"cw"},{"z":17,"isotope":35},{"z":9},{"z":1},{"z":1}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[1,3]},{"atoms":[0,4]},{"atoms":[1,5]}],"conformers":[{"dim":2,"coords":[[-1.1987,-0.0452],[-0.3332,0.4555],[0.1659,1.322],[0.5332,-0.0438],[-2.0652,0.4541],[-0.8339,1.3212]]},{"dim":3,"coords":[[0.9553,-0.3743,-0.4679],[-0.3616,-0.131,-0.0794],[-0.5097,1.6255,0.1705],[-0.5778,-0.7919,1.1042],[1.5276,0.1063,0.1627],[-1.0339,-0.4345,-0.8902]]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.2","cipCodes":[[1,"S"]]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2024.09.2","values":[-0.352,0.273,-0.055,-0.198,0.215,0.117]}]}]} -186: [02:23:32] done -186: [02:23:32] test4: writing properties +186: [23:10:50] done +186: [23:10:50] test4: writing properties 186: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"atoms":[{"impHs":3},{"impHs":3}],"bonds":[{"atoms":[0,1]}],"properties":{"foo_string":"bar","foo_int":1,"foo_double":1.2},"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.2","cipRanks":[0,0]}]}]} -186: [02:23:32] done -186: [02:23:32] test5: writing partial charges +186: [23:10:50] done +186: [23:10:50] test5: writing partial charges 186: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"atoms":[{"impHs":3},{"z":8,"impHs":1}],"bonds":[{"atoms":[0,1]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.2","cipRanks":[0,1]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2024.09.2","values":[0.5,-0.5]}]}]} -186: [02:23:32] testing parse options -186: [02:23:32] done -186: [02:23:32] testing github #2046: CIPRank values from JSONDataToMols are not unsigned +186: [23:10:50] testing parse options +186: [23:10:50] done +186: [23:10:50] testing github #2046: CIPRank values from JSONDataToMols are not unsigned 186: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":2},{"impHs":2},{"impHs":2},{"z":8},{"impHs":1,"stereo":"cw"},{"z":9}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[2,3]},{"atoms":[3,4]},{"atoms":[4,5]},{"atoms":[4,0]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.2","cipRanks":[1,0,2,4,3,5],"cipCodes":[[4,"S"]],"atomRings":[[0,1,2,3,4]]}]}]} -186: [02:23:32] done -186: [02:23:32] testing 'either' stereochemistry -186: [02:23:32] done -175/230 Test #186: molInterchangeTest1 .................... Passed 0.12 sec +186: [23:10:50] done +186: [23:10:50] testing 'either' stereochemistry +186: [23:10:50] done +175/230 Test #186: molInterchangeTest1 .................... Passed 0.10 sec test 187 Start 187: molInterchangeCatchTest 187: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeCatchTest 187: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange 187: Test timeout computed to be: 1500 -187: Randomness seeded to: 3998320238 -187: [02:23:32] unrecognized bond type 12 set to zero while writing -187: [02:23:32] unrecognized bond type 0 set to zero while writing +187: Randomness seeded to: 4164630669 +187: [23:10:51] unrecognized bond type 12 set to zero while writing +187: [23:10:51] unrecognized bond type 0 set to zero while writing 187: =============================================================================== 187: All tests passed (122 assertions in 6 test cases) 187: -176/230 Test #187: molInterchangeCatchTest ................ Passed 0.08 sec +176/230 Test #187: molInterchangeCatchTest ................ Passed 0.11 sec test 188 Start 188: pyMolInterchange 188: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolInterchange/Wrap/testMolInterchange.py" 188: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/Wrap 188: Test timeout computed to be: 1500 -179: [02:23:32] ------------------------------------- -179: [02:23:32] testTautomerQueries -148: --------------------------------- -148: test O3A multithreading bug -148: -148: --------------------------------- -148: testCrippenO3A multithreading -148: -148: generating reference data -179: [02:23:32] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... -179: [02:23:32] ------------------------------------- -179: [02:23:32] github3881 recursive smarts with rings -177/230 Test #179: substructLibraryTest ................... Passed 13.83 sec +188: .. +188: ---------------------------------------------------------------------- +188: Ran 2 tests in 0.027s +188: +188: OK +185: .................... +185: ---------------------------------------------------------------------- +185: Ran 20 tests in 2.484s +185: +185: OK +177/230 Test #188: pyMolInterchange ....................... Passed 1.15 sec test 189 Start 189: testSLNParse @@ -32439,119 +32494,100 @@ 189: 2 0->3 order: 1 189: 3 0->4 order: 1 189: 4 0->5 order: 1 -189: [02:23:32] SLN Parse Error: syntax error while parsing: CH4[I=13] -189: [02:23:32] Failed parsing SLN 'CH4[I=13]' -189: [02:23:32] SLN Parser error: Atom ID 1 appears *after* its ring closure. -189: [02:23:32] SLN Parser error: Ring closure 1 does not have a corresponding opener. -189: [02:23:32] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) -189: [02:23:32] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' -189: [02:23:32] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) -189: [02:23:32] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' -189: [02:23:32] SLN Parse Error: syntax error while parsing: CH4 fff -189: [02:23:32] Failed parsing SLN 'CH4 fff' -189: [02:23:32] SLN Parse Error: syntax error while parsing: C[charge=+1] foo -189: [02:23:32] Failed parsing SLN 'C[charge=+1] foo' -189: [02:23:32] Query property 'is' ignored on non-query atom -189: [02:23:32] Query property 'is' ignored on non-query atom -178/230 Test #189: testSLNParse ........................... Passed 0.03 sec +189: [23:10:52] SLN Parse Error: syntax error while parsing: CH4[I=13] +189: [23:10:52] Failed parsing SLN 'CH4[I=13]' +189: [23:10:52] SLN Parser error: Atom ID 1 appears *after* its ring closure. +189: [23:10:52] SLN Parser error: Ring closure 1 does not have a corresponding opener. +189: [23:10:52] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) +189: [23:10:52] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' +189: [23:10:52] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) +189: [23:10:52] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' +189: [23:10:52] SLN Parse Error: syntax error while parsing: CH4 fff +189: [23:10:52] Failed parsing SLN 'CH4 fff' +189: [23:10:52] SLN Parse Error: syntax error while parsing: C[charge=+1] foo +189: [23:10:52] Failed parsing SLN 'C[charge=+1] foo' +189: [23:10:52] Query property 'is' ignored on non-query atom +189: [23:10:52] Query property 'is' ignored on non-query atom +178/230 Test #189: testSLNParse ........................... Passed 0.07 sec test 190 Start 190: pySLNParse 190: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/SLNParse/Wrap/testSLN.py" 190: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse/Wrap 190: Test timeout computed to be: 1500 -188: .. -188: ---------------------------------------------------------------------- -188: Ran 2 tests in 0.023s -188: -188: OK -179/230 Test #188: pyMolInterchange ....................... Passed 0.46 sec +179/230 Test #185: pyRGroupDecomposition .................. Passed 3.55 sec test 191 Start 191: pyGraphMolWrap 191: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/rough_test.py" 191: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 191: Test timeout computed to be: 1500 -146: .........[02:23:32] Molecule does not have explicit Hs. Consider calling AddHs() -146: .[02:23:32] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:23:32] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:23:32] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:23:32] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:23:32] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:23:32] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:23:32] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:23:32] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:23:32] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:23:32] Molecule does not have explicit Hs. Consider calling AddHs() -146: .[02:23:32] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:23:32] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:23:32] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:23:32] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:23:32] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:23:32] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:23:32] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:23:32] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:23:32] Molecule does not have explicit Hs. Consider calling AddHs() -146: [02:23:32] Molecule does not have explicit Hs. Consider calling AddHs() 190: .. 190: ---------------------------------------------------------------------- -190: Ran 2 tests in 0.015s +190: Ran 2 tests in 0.022s 190: 190: OK -182: bulk -148: processing -148: launch :0 -148: launch :1 -148: launch :2 -148: launch :3 -180/230 Test #190: pySLNParse ............................. Passed 0.71 sec +182: bulk, no symmetry +180/230 Test #190: pySLNParse ............................. Passed 1.09 sec test 192 Start 192: pyTestConformerWrap 192: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/testConformer.py" 192: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 192: Test timeout computed to be: 1500 -191: ..............[02:23:33] SMARTS Parse Error: syntax error while parsing: fiib -191: [02:23:33] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' -191: ....[02:23:33] ERROR: Problems encountered parsing data fields -191: [02:23:33] ERROR: moving to the beginning of the next molecule -191: [02:23:33] ERROR: Problems encountered parsing data fields -191: [02:23:33] ERROR: moving to the beginning of the next molecule -191: [02:23:33] Spurious data before the first property will be ignored -191: [02:23:33] Property will be truncated after the first blank line -191: [02:23:33] Property will be truncated after the first blank line -191: [02:23:33] Property will be truncated after the first blank line -191: [02:23:33] ERROR: Problems encountered parsing data fields -191: [02:23:33] ERROR: moving to the beginning of the next molecule -191: [02:23:33] ERROR: Problems encountered parsing data fields -191: [02:23:33] ERROR: moving to the beginning of the next molecule -191: [02:23:33] Spurious data before the first property will be ignored -191: [02:23:33] Property will be truncated after the first blank line -191: [02:23:33] Property will be truncated after the first blank line -191: [02:23:33] Property will be truncated after the first blank line -191: [02:23:33] ERROR: Problems encountered parsing data fields -191: [02:23:33] ERROR: moving to the beginning of the next molecule -191: [02:23:33] Property will be truncated after the first blank line -191: [02:23:33] ERROR: Problems encountered parsing data fields -191: [02:23:33] ERROR: moving to the beginning of the next molecule -191: [02:23:33] Property will be truncated after the first blank line -191: .[02:23:33] SMILES Parse Error: syntax error while parsing: fail -191: [02:23:33] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -191: [02:23:33] ERROR: Smiles parse error on line 2 -191: [02:23:33] ERROR: Cannot create molecule from : 'fail' +191: ..............[23:10:53] SMARTS Parse Error: syntax error while parsing: fiib +191: [23:10:53] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' +191: ....[23:10:53] ERROR: Problems encountered parsing data fields +191: [23:10:53] ERROR: moving to the beginning of the next molecule +191: [23:10:53] ERROR: Problems encountered parsing data fields +191: [23:10:53] ERROR: moving to the beginning of the next molecule +191: [23:10:53] Spurious data before the first property will be ignored +191: [23:10:53] Property will be truncated after the first blank line +191: [23:10:53] Property will be truncated after the first blank line +191: [23:10:53] Property will be truncated after the first blank line +191: [23:10:54] ERROR: Problems encountered parsing data fields +191: [23:10:54] ERROR: moving to the beginning of the next molecule +191: [23:10:54] ERROR: Problems encountered parsing data fields +191: [23:10:54] ERROR: moving to the beginning of the next molecule +191: [23:10:54] Spurious data before the first property will be ignored +191: [23:10:54] Property will be truncated after the first blank line +191: [23:10:54] Property will be truncated after the first blank line +191: [23:10:54] Property will be truncated after the first blank line +191: [23:10:54] ERROR: Problems encountered parsing data fields +191: [23:10:54] ERROR: moving to the beginning of the next molecule +191: [23:10:54] Property will be truncated after the first blank line +191: [23:10:54] ERROR: Problems encountered parsing data fields +191: [23:10:54] ERROR: moving to the beginning of the next molecule +191: [23:10:54] Property will be truncated after the first blank line +191: .[23:10:54] SMILES Parse Error: syntax error while parsing: fail +191: [23:10:54] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +191: [23:10:54] ERROR: Smiles parse error on line 2 +191: [23:10:54] ERROR: Cannot create molecule from : 'fail' 191: >>> This may result in an infinite loop. It should finish almost instantly 191: <<< OK, it finished. -191: ............[02:23:33] Explicit valence for atom # 1 C, 5, is greater than permitted -191: ......[02:23:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -191: [02:23:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -191: [02:23:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -191: [02:23:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +192: ...... +192: ---------------------------------------------------------------------- +192: Ran 6 tests in 0.025s +192: +192: OK +191: ............[23:10:54] Explicit valence for atom # 1 C, 5, is greater than permitted +191: ......[23:10:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +191: [23:10:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +191: [23:10:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +191: [23:10:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 191: .inWedges: [H]C12C3([H])C4([H])C1([H])C1([H])C2([H])C3([H])C41[H] |(-0.612,-0.6446,0.635;0.0021,-0.0041,0.002;-0.0187,1.5258,0.0104;-0.6498,2.1424,0.6504;1.5111,1.5466,-0.0041;2.1372,2.1804,0.624;1.5319,0.0168,-0.0125;2.175,-0.6067,0.6086;1.5173,0.025,-1.5424;2.1484,-0.5936,-2.1805;-0.0125,0.0041,-1.5279;-0.6405,-0.6297,-2.154;-0.0333,1.534,-1.5195;-0.6783,2.1574,-2.1387;1.4965,1.5548,-1.534;2.1106,2.1972,-2.1651)| -191: ........[02:23:33] non-ring atom 0 marked aromatic -191: [02:23:33] non-ring atom 0 marked aromatic -191: [02:23:33] +191: ........[23:10:54] non-ring atom 0 marked aromatic +191: [23:10:54] non-ring atom 0 marked aromatic +191: [23:10:54] 191: 191: **** +181/230 Test #192: pyTestConformerWrap .................... Passed 0.86 sec +test 193 + Start 193: pyTestTrajectory + +193: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/testTrajectory.py" +193: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Wrap +193: Test timeout computed to be: 1500 191: Range Error 191: idx 191: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp @@ -32562,9 +32598,9 @@ 191: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 191: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 191: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -191: 4# 0x0000FFFF99CAB690 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 4# 0x0000FFFF90C5B690 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 191: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -191: 6# 0x0000FFFF9C3715C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +191: 6# 0x0000FFFF933215C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 191: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 191: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 191: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -32575,17 +32611,17 @@ 191: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 191: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 17# 0x0000FFFF99BE4180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 18# 0x0000FFFF99BE4118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 19# 0x0000FFFF99BE40A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 20# 0x0000FFFF99BE4040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 21# 0x0000FFFF99BE3FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 17# 0x0000FFFF90B94180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 18# 0x0000FFFF90B94118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 19# 0x0000FFFF90B940A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 20# 0x0000FFFF90B94040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 21# 0x0000FFFF90B93FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 191: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -191: 27# 0x0000FFFF9C36E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +191: 27# 0x0000FFFF9331E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 191: 28# _PyObject_MakeTpCall in /usr/bin/python3 191: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 30# 0x00000000004C3D1C in /usr/bin/python3 @@ -32618,15 +32654,15 @@ 191: 57# _PyRun_AnyFileObject in /usr/bin/python3 191: 58# Py_RunMain in /usr/bin/python3 191: 59# Py_BytesMain in /usr/bin/python3 -191: 60# 0x0000FFFF9CCE229C in /lib/aarch64-linux-gnu/libc.so.6 +191: 60# 0x0000FFFF93C9229C in /lib/aarch64-linux-gnu/libc.so.6 191: 61# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 191: 62# _start in /usr/bin/python3 191: ---------- 191: **** 191: -191: [02:23:33] non-ring atom 0 marked aromatic -191: [02:23:33] non-ring atom 0 marked aromatic -191: [02:23:33] +191: [23:10:54] non-ring atom 0 marked aromatic +191: [23:10:54] non-ring atom 0 marked aromatic +191: [23:10:54] 191: 191: **** 191: Range Error @@ -32639,9 +32675,9 @@ 191: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 191: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 191: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -191: 4# 0x0000FFFF99CAB690 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 4# 0x0000FFFF90C5B690 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 191: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -191: 6# 0x0000FFFF9C3715C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +191: 6# 0x0000FFFF933215C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 191: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 191: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 191: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -32652,17 +32688,17 @@ 191: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 191: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 17# 0x0000FFFF99BE4180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 18# 0x0000FFFF99BE4118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 19# 0x0000FFFF99BE40A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 20# 0x0000FFFF99BE4040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 21# 0x0000FFFF99BE3FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 17# 0x0000FFFF90B94180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 18# 0x0000FFFF90B94118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 19# 0x0000FFFF90B940A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 20# 0x0000FFFF90B94040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 21# 0x0000FFFF90B93FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 191: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -191: 27# 0x0000FFFF9C36E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +191: 27# 0x0000FFFF9331E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 191: 28# _PyObject_MakeTpCall in /usr/bin/python3 191: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 30# 0x00000000004C3D1C in /usr/bin/python3 @@ -32695,29 +32731,18 @@ 191: 57# _PyRun_AnyFileObject in /usr/bin/python3 191: 58# Py_RunMain in /usr/bin/python3 191: 59# Py_BytesMain in /usr/bin/python3 -191: 60# 0x0000FFFF9CCE229C in /lib/aarch64-linux-gnu/libc.so.6 +191: 60# 0x0000FFFF93C9229C in /lib/aarch64-linux-gnu/libc.so.6 191: 61# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 191: 62# _start in /usr/bin/python3 191: ---------- 191: **** 191: -191: ...............[02:23:33] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. -191: [02:23:33] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. -191: ..............[02:23:33] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -191: [02:23:33] Explicit valence for atom # 1 C, 5, is greater than permitted -192: ...... -192: ---------------------------------------------------------------------- -192: Ran 6 tests in 0.009s -192: -192: OK -181/230 Test #192: pyTestConformerWrap .................... Passed 0.67 sec -test 193 - Start 193: pyTestTrajectory - -193: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/testTrajectory.py" -193: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Wrap -193: Test timeout computed to be: 1500 -193: [02:23:34] +191: ...............[23:10:54] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. +191: [23:10:54] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. +191: ..............[23:10:54] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +191: [23:10:54] Explicit valence for atom # 1 C, 5, is greater than permitted +182: [23:10:54] Relabelling existing label +193: [23:10:55] 193: 193: **** 193: Pre-condition Violation @@ -32731,23 +32756,23 @@ 193: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 193: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -193: 5# 0x0000FFFFA7CE15C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +193: 5# 0x0000FFFFADD515C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 193: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 193: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 193: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 11# 0x0000FFFFA57C4180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 12# 0x0000FFFFA57C4118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 13# 0x0000FFFFA57C40A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 14# 0x0000FFFFA57C4040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 15# 0x0000FFFFA57C3FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 11# 0x0000FFFFAB834180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 12# 0x0000FFFFAB834118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 13# 0x0000FFFFAB8340A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 14# 0x0000FFFFAB834040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 15# 0x0000FFFFAB833FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 193: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -193: 21# 0x0000FFFFA7CDE19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +193: 21# 0x0000FFFFADD4E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 193: 22# _PyObject_MakeTpCall in /usr/bin/python3 193: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 24# 0x00000000004C3D1C in /usr/bin/python3 @@ -32780,13 +32805,13 @@ 193: 51# _PyRun_AnyFileObject in /usr/bin/python3 193: 52# Py_RunMain in /usr/bin/python3 193: 53# Py_BytesMain in /usr/bin/python3 -193: 54# 0x0000FFFFA84C229C in /lib/aarch64-linux-gnu/libc.so.6 +193: 54# 0x0000FFFFAE53229C in /lib/aarch64-linux-gnu/libc.so.6 193: 55# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 193: 56# _start in /usr/bin/python3 193: ---------- 193: **** 193: -193: .[02:23:34] +193: .[23:10:55] 193: 193: **** 193: Pre-condition Violation @@ -32800,23 +32825,23 @@ 193: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 193: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -193: 5# 0x0000FFFFA7CE15C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +193: 5# 0x0000FFFFADD515C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 193: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 193: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 193: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 11# 0x0000FFFFA57C4180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 12# 0x0000FFFFA57C4118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 13# 0x0000FFFFA57C40A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 14# 0x0000FFFFA57C4040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 15# 0x0000FFFFA57C3FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 11# 0x0000FFFFAB834180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 12# 0x0000FFFFAB834118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 13# 0x0000FFFFAB8340A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 14# 0x0000FFFFAB834040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 15# 0x0000FFFFAB833FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 193: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -193: 21# 0x0000FFFFA7CDE19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +193: 21# 0x0000FFFFADD4E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 193: 22# _PyObject_MakeTpCall in /usr/bin/python3 193: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 24# 0x00000000004C3D1C in /usr/bin/python3 @@ -32849,13 +32874,97 @@ 193: 51# _PyRun_AnyFileObject in /usr/bin/python3 193: 52# Py_RunMain in /usr/bin/python3 193: 53# Py_BytesMain in /usr/bin/python3 -193: 54# 0x0000FFFFA84C229C in /lib/aarch64-linux-gnu/libc.so.6 +193: 54# 0x0000FFFFAE53229C in /lib/aarch64-linux-gnu/libc.so.6 193: 55# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 193: 56# _start in /usr/bin/python3 193: ---------- 193: **** 193: -193: .[02:23:34] +182: Best mapping +182/230 Test #182: testRGroupDecomp ....................... Passed 11.07 sec +test 194 + Start 194: pyTestSGroups + +194: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/testSGroups.py" +194: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Wrap +194: Test timeout computed to be: 1500 +191: ............................[23:10:55] unable to set wavy bonds for double bonds: 3 +191: .............[23:10:55] +191: +191: **** +191: Range Error +191: idx +191: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp +191: Failed Expression: 6 < 5 +191: ---------- +191: Stacktrace: +191: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +191: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +191: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +191: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +191: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +191: 6# 0x0000FFFF933215C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +191: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +191: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so +191: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +191: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +191: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so +191: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so +191: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +191: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +191: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +191: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 17# 0x0000FFFF90B94180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 18# 0x0000FFFF90B94118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 19# 0x0000FFFF90B940A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 20# 0x0000FFFF90B94040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 21# 0x0000FFFF90B93FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so +191: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so +191: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so +191: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so +191: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +191: 27# 0x0000FFFF9331E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +191: 28# _PyObject_MakeTpCall in /usr/bin/python3 +191: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 +191: 30# 0x00000000004C3D1C in /usr/bin/python3 +191: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 +191: 32# _PyObject_Call_Prepend in /usr/bin/python3 +191: 33# 0x000000000052608C in /usr/bin/python3 +191: 34# _PyObject_MakeTpCall in /usr/bin/python3 +191: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 +191: 36# 0x00000000004C3D1C in /usr/bin/python3 +191: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 +191: 38# _PyObject_Call_Prepend in /usr/bin/python3 +191: 39# 0x000000000052608C in /usr/bin/python3 +191: 40# _PyObject_MakeTpCall in /usr/bin/python3 +191: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 +191: 42# 0x00000000004C3D1C in /usr/bin/python3 +191: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 +191: 44# _PyObject_Call_Prepend in /usr/bin/python3 +191: 45# 0x000000000052608C in /usr/bin/python3 +191: 46# _PyObject_MakeTpCall in /usr/bin/python3 +191: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 +191: 48# _PyObject_Call_Prepend in /usr/bin/python3 +191: 49# 0x000000000051FB4C in /usr/bin/python3 +191: 50# 0x000000000051B324 in /usr/bin/python3 +191: 51# _PyObject_MakeTpCall in /usr/bin/python3 +191: 52# _PyEval_EvalFrameDefault in /usr/bin/python3 +191: 53# PyEval_EvalCode in /usr/bin/python3 +191: 54# 0x0000000000595200 in /usr/bin/python3 +191: 55# 0x00000000006757AC in /usr/bin/python3 +191: 56# _PyRun_SimpleFileObject in /usr/bin/python3 +191: 57# _PyRun_AnyFileObject in /usr/bin/python3 +191: 58# Py_RunMain in /usr/bin/python3 +191: 59# Py_BytesMain in /usr/bin/python3 +191: 60# 0x0000FFFF93C9229C in /lib/aarch64-linux-gnu/libc.so.6 +191: 61# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +191: 62# _start in /usr/bin/python3 +191: ---------- +191: **** +191: +193: .[23:10:55] 193: 193: **** 193: Range Error @@ -32870,23 +32979,23 @@ 193: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -193: 6# 0x0000FFFFA7CE15C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +193: 6# 0x0000FFFFADD515C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 193: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 193: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 193: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 12# 0x0000FFFFA57C4180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 13# 0x0000FFFFA57C4118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 14# 0x0000FFFFA57C40A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 15# 0x0000FFFFA57C4040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 16# 0x0000FFFFA57C3FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 12# 0x0000FFFFAB834180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 13# 0x0000FFFFAB834118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 14# 0x0000FFFFAB8340A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 15# 0x0000FFFFAB834040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 16# 0x0000FFFFAB833FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 193: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 21# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -193: 22# 0x0000FFFFA7CDE19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +193: 22# 0x0000FFFFADD4E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 193: 23# _PyObject_MakeTpCall in /usr/bin/python3 193: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 25# 0x00000000004C3D1C in /usr/bin/python3 @@ -32919,13 +33028,13 @@ 193: 52# _PyRun_AnyFileObject in /usr/bin/python3 193: 53# Py_RunMain in /usr/bin/python3 193: 54# Py_BytesMain in /usr/bin/python3 -193: 55# 0x0000FFFFA84C229C in /lib/aarch64-linux-gnu/libc.so.6 +193: 55# 0x0000FFFFAE53229C in /lib/aarch64-linux-gnu/libc.so.6 193: 56# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 193: 57# _start in /usr/bin/python3 193: ---------- 193: **** 193: -193: .[02:23:34] +193: .[23:10:55] 193: 193: **** 193: Pre-condition Violation @@ -32939,23 +33048,23 @@ 193: 2# RDKit::readAmberTrajectory(std::__cxx11::basic_string, std::allocator > const&, RDKit::Trajectory&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 193: 3# boost::python::objects::caller_py_function_impl, std::allocator > const&, RDKit::Trajectory&), boost::python::default_call_policies, boost::mpl::vector3, std::allocator > const&, RDKit::Trajectory&> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -193: 5# 0x0000FFFFA7CE15C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +193: 5# 0x0000FFFFADD515C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 193: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 193: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 193: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 11# 0x0000FFFFA57C4180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 12# 0x0000FFFFA57C4118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 13# 0x0000FFFFA57C40A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 14# 0x0000FFFFA57C4040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 15# 0x0000FFFFA57C3FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 11# 0x0000FFFFAB834180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 12# 0x0000FFFFAB834118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 13# 0x0000FFFFAB8340A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 14# 0x0000FFFFAB834040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 15# 0x0000FFFFAB833FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 193: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -193: 21# 0x0000FFFFA7CDE19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +193: 21# 0x0000FFFFADD4E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 193: 22# _PyObject_MakeTpCall in /usr/bin/python3 193: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 24# 0x00000000004C3D1C in /usr/bin/python3 @@ -32988,13 +33097,13 @@ 193: 51# _PyRun_AnyFileObject in /usr/bin/python3 193: 52# Py_RunMain in /usr/bin/python3 193: 53# Py_BytesMain in /usr/bin/python3 -193: 54# 0x0000FFFFA84C229C in /lib/aarch64-linux-gnu/libc.so.6 +193: 54# 0x0000FFFFAE53229C in /lib/aarch64-linux-gnu/libc.so.6 193: 55# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 193: 56# _start in /usr/bin/python3 193: ---------- 193: **** 193: -193: ..[02:23:34] +193: ..[23:10:55] 193: 193: **** 193: Pre-condition Violation @@ -33008,23 +33117,23 @@ 193: 2# RDKit::readGromosTrajectory(std::__cxx11::basic_string, std::allocator > const&, RDKit::Trajectory&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 193: 3# boost::python::objects::caller_py_function_impl, std::allocator > const&, RDKit::Trajectory&), boost::python::default_call_policies, boost::mpl::vector3, std::allocator > const&, RDKit::Trajectory&> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -193: 5# 0x0000FFFFA7CE15C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +193: 5# 0x0000FFFFADD515C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 193: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 193: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 193: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 11# 0x0000FFFFA57C4180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 12# 0x0000FFFFA57C4118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 13# 0x0000FFFFA57C40A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 14# 0x0000FFFFA57C4040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 15# 0x0000FFFFA57C3FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 11# 0x0000FFFFAB834180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 12# 0x0000FFFFAB834118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 13# 0x0000FFFFAB8340A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 14# 0x0000FFFFAB834040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 15# 0x0000FFFFAB833FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 193: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -193: 21# 0x0000FFFFA7CDE19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +193: 21# 0x0000FFFFADD4E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 193: 22# _PyObject_MakeTpCall in /usr/bin/python3 193: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 24# 0x00000000004C3D1C in /usr/bin/python3 @@ -33057,13 +33166,13 @@ 193: 51# _PyRun_AnyFileObject in /usr/bin/python3 193: 52# Py_RunMain in /usr/bin/python3 193: 53# Py_BytesMain in /usr/bin/python3 -193: 54# 0x0000FFFFA84C229C in /lib/aarch64-linux-gnu/libc.so.6 +193: 54# 0x0000FFFFAE53229C in /lib/aarch64-linux-gnu/libc.so.6 193: 55# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 193: 56# _start in /usr/bin/python3 193: ---------- 193: **** 193: -193: .[02:23:34] +193: .[23:10:55] 193: 193: **** 193: Pre-condition Violation @@ -33077,23 +33186,23 @@ 193: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 193: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -193: 5# 0x0000FFFFA7CE15C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +193: 5# 0x0000FFFFADD515C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 193: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 193: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 193: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 11# 0x0000FFFFA57C4180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 12# 0x0000FFFFA57C4118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 13# 0x0000FFFFA57C40A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 14# 0x0000FFFFA57C4040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 15# 0x0000FFFFA57C3FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 11# 0x0000FFFFAB834180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 12# 0x0000FFFFAB834118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 13# 0x0000FFFFAB8340A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 14# 0x0000FFFFAB834040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 15# 0x0000FFFFAB833FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 193: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -193: 21# 0x0000FFFFA7CDE19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +193: 21# 0x0000FFFFADD4E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 193: 22# _PyObject_MakeTpCall in /usr/bin/python3 193: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 24# 0x00000000004C3D1C in /usr/bin/python3 @@ -33126,13 +33235,13 @@ 193: 51# _PyRun_AnyFileObject in /usr/bin/python3 193: 52# Py_RunMain in /usr/bin/python3 193: 53# Py_BytesMain in /usr/bin/python3 -193: 54# 0x0000FFFFA84C229C in /lib/aarch64-linux-gnu/libc.so.6 +193: 54# 0x0000FFFFAE53229C in /lib/aarch64-linux-gnu/libc.so.6 193: 55# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 193: 56# _start in /usr/bin/python3 193: ---------- 193: **** 193: -193: [02:23:34] +193: [23:10:55] 193: 193: **** 193: Pre-condition Violation @@ -33146,23 +33255,23 @@ 193: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 193: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -193: 5# 0x0000FFFFA7CE15C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +193: 5# 0x0000FFFFADD515C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 193: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 193: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 193: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 11# 0x0000FFFFA57C4180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 12# 0x0000FFFFA57C4118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 13# 0x0000FFFFA57C40A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 14# 0x0000FFFFA57C4040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 15# 0x0000FFFFA57C3FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 11# 0x0000FFFFAB834180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 12# 0x0000FFFFAB834118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 13# 0x0000FFFFAB8340A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 14# 0x0000FFFFAB834040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 15# 0x0000FFFFAB833FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 193: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -193: 21# 0x0000FFFFA7CDE19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +193: 21# 0x0000FFFFADD4E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 193: 22# _PyObject_MakeTpCall in /usr/bin/python3 193: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 24# 0x00000000004C3D1C in /usr/bin/python3 @@ -33195,13 +33304,13 @@ 193: 51# _PyRun_AnyFileObject in /usr/bin/python3 193: 52# Py_RunMain in /usr/bin/python3 193: 53# Py_BytesMain in /usr/bin/python3 -193: 54# 0x0000FFFFA84C229C in /lib/aarch64-linux-gnu/libc.so.6 +193: 54# 0x0000FFFFAE53229C in /lib/aarch64-linux-gnu/libc.so.6 193: 55# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 193: 56# _start in /usr/bin/python3 193: ---------- 193: **** 193: -193: .[02:23:34] +193: .[23:10:55] 193: 193: **** 193: Range Error @@ -33216,23 +33325,23 @@ 193: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -193: 6# 0x0000FFFFA7CE15C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +193: 6# 0x0000FFFFADD515C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 193: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 193: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 193: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 12# 0x0000FFFFA57C4180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 13# 0x0000FFFFA57C4118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 14# 0x0000FFFFA57C40A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 15# 0x0000FFFFA57C4040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 16# 0x0000FFFFA57C3FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 12# 0x0000FFFFAB834180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 13# 0x0000FFFFAB834118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 14# 0x0000FFFFAB8340A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 15# 0x0000FFFFAB834040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 16# 0x0000FFFFAB833FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 193: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 21# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -193: 22# 0x0000FFFFA7CDE19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +193: 22# 0x0000FFFFADD4E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 193: 23# _PyObject_MakeTpCall in /usr/bin/python3 193: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 25# 0x00000000004C3D1C in /usr/bin/python3 @@ -33265,13 +33374,13 @@ 193: 52# _PyRun_AnyFileObject in /usr/bin/python3 193: 53# Py_RunMain in /usr/bin/python3 193: 54# Py_BytesMain in /usr/bin/python3 -193: 55# 0x0000FFFFA84C229C in /lib/aarch64-linux-gnu/libc.so.6 +193: 55# 0x0000FFFFAE53229C in /lib/aarch64-linux-gnu/libc.so.6 193: 56# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 193: 57# _start in /usr/bin/python3 193: ---------- 193: **** 193: -193: [02:23:34] +193: [23:10:55] 193: 193: **** 193: Range Error @@ -33285,23 +33394,23 @@ 193: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 193: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -193: 5# 0x0000FFFFA7CE15C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +193: 5# 0x0000FFFFADD515C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 193: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 193: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 193: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 11# 0x0000FFFFA57C4180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 12# 0x0000FFFFA57C4118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 13# 0x0000FFFFA57C40A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 14# 0x0000FFFFA57C4040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 15# 0x0000FFFFA57C3FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 11# 0x0000FFFFAB834180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 12# 0x0000FFFFAB834118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 13# 0x0000FFFFAB8340A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 14# 0x0000FFFFAB834040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 15# 0x0000FFFFAB833FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 193: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -193: 21# 0x0000FFFFA7CDE19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +193: 21# 0x0000FFFFADD4E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 193: 22# _PyObject_MakeTpCall in /usr/bin/python3 193: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 24# 0x00000000004C3D1C in /usr/bin/python3 @@ -33334,16 +33443,15 @@ 193: 51# _PyRun_AnyFileObject in /usr/bin/python3 193: 52# Py_RunMain in /usr/bin/python3 193: 53# Py_BytesMain in /usr/bin/python3 -193: 54# 0x0000FFFFA84C229C in /lib/aarch64-linux-gnu/libc.so.6 +193: 54# 0x0000FFFFAE53229C in /lib/aarch64-linux-gnu/libc.so.6 193: 55# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 193: 56# _start in /usr/bin/python3 193: ---------- 193: **** 193: -193: .[02:23:34] +193: .[23:10:55] 193: 193: **** -191: ............................[02:23:34] unable to set wavy bonds for double bonds: 3 193: Range Error 193: snapshotNum 193: Violation occurred on line 71 in file ./Code/GraphMol/Trajectory/Trajectory.cpp @@ -33356,23 +33464,23 @@ 193: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -193: 6# 0x0000FFFFA7CE15C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +193: 6# 0x0000FFFFADD515C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 193: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 193: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 193: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 12# 0x0000FFFFA57C4180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 13# 0x0000FFFFA57C4118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 14# 0x0000FFFFA57C40A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 15# 0x0000FFFFA57C4040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 16# 0x0000FFFFA57C3FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 12# 0x0000FFFFAB834180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 13# 0x0000FFFFAB834118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 14# 0x0000FFFFAB8340A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 15# 0x0000FFFFAB834040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 16# 0x0000FFFFAB833FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 193: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 21# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -193: 22# 0x0000FFFFA7CDE19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +193: 22# 0x0000FFFFADD4E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 193: 23# _PyObject_MakeTpCall in /usr/bin/python3 193: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 25# 0x00000000004C3D1C in /usr/bin/python3 @@ -33405,13 +33513,13 @@ 193: 52# _PyRun_AnyFileObject in /usr/bin/python3 193: 53# Py_RunMain in /usr/bin/python3 193: 54# Py_BytesMain in /usr/bin/python3 -193: 55# 0x0000FFFFA84C229C in /lib/aarch64-linux-gnu/libc.so.6 +193: 55# 0x0000FFFFAE53229C in /lib/aarch64-linux-gnu/libc.so.6 193: 56# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 193: 57# _start in /usr/bin/python3 193: ---------- 193: **** 193: -193: [02:23:34] +193: [23:10:55] 193: 193: **** 193: Pre-condition Violation @@ -33425,23 +33533,23 @@ 193: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 193: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -193: 5# 0x0000FFFFA7CE15C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +193: 5# 0x0000FFFFADD515C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 193: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 193: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 193: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 11# 0x0000FFFFA57C4180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 12# 0x0000FFFFA57C4118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 13# 0x0000FFFFA57C40A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 14# 0x0000FFFFA57C4040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 15# 0x0000FFFFA57C3FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 11# 0x0000FFFFAB834180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 12# 0x0000FFFFAB834118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 13# 0x0000FFFFAB8340A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 14# 0x0000FFFFAB834040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 15# 0x0000FFFFAB833FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 193: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -193: 21# 0x0000FFFFA7CDE19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +193: 21# 0x0000FFFFADD4E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 193: 22# _PyObject_MakeTpCall in /usr/bin/python3 193: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 24# 0x00000000004C3D1C in /usr/bin/python3 @@ -33474,13 +33582,13 @@ 193: 51# _PyRun_AnyFileObject in /usr/bin/python3 193: 52# Py_RunMain in /usr/bin/python3 193: 53# Py_BytesMain in /usr/bin/python3 -193: 54# 0x0000FFFFA84C229C in /lib/aarch64-linux-gnu/libc.so.6 +193: 54# 0x0000FFFFAE53229C in /lib/aarch64-linux-gnu/libc.so.6 193: 55# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 193: 56# _start in /usr/bin/python3 193: ---------- 193: **** 193: -193: [02:23:34] +193: [23:10:55] 193: 193: **** 193: Pre-condition Violation @@ -33494,23 +33602,23 @@ 193: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 193: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 193: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -193: 5# 0x0000FFFFA7CE15C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +193: 5# 0x0000FFFFADD515C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 193: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 193: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 193: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 193: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 11# 0x0000FFFFA57C4180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 12# 0x0000FFFFA57C4118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 13# 0x0000FFFFA57C40A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 14# 0x0000FFFFA57C4040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -193: 15# 0x0000FFFFA57C3FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 11# 0x0000FFFFAB834180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 12# 0x0000FFFFAB834118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 13# 0x0000FFFFAB8340A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 14# 0x0000FFFFAB834040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +193: 15# 0x0000FFFFAB833FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 193: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 193: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -193: 21# 0x0000FFFFA7CDE19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +193: 21# 0x0000FFFFADD4E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 193: 22# _PyObject_MakeTpCall in /usr/bin/python3 193: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 193: 24# 0x00000000004C3D1C in /usr/bin/python3 @@ -33543,7 +33651,7 @@ 193: 51# _PyRun_AnyFileObject in /usr/bin/python3 193: 52# Py_RunMain in /usr/bin/python3 193: 53# Py_BytesMain in /usr/bin/python3 -193: 54# 0x0000FFFFA84C229C in /lib/aarch64-linux-gnu/libc.so.6 +193: 54# 0x0000FFFFAE53229C in /lib/aarch64-linux-gnu/libc.so.6 193: 55# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 193: 56# _start in /usr/bin/python3 193: ---------- @@ -33551,113 +33659,24 @@ 193: 193: . 193: ---------------------------------------------------------------------- -193: Ran 9 tests in 0.386s +193: Ran 9 tests in 0.779s 193: 193: OK 193: Testing Trajectory wrapper -191: .............[02:23:34] -191: -191: **** -191: Range Error -191: idx -191: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp -191: Failed Expression: 6 < 5 -191: ---------- -191: Stacktrace: -191: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -191: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -191: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -191: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -191: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -191: 6# 0x0000FFFF9C3715C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -191: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -191: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so -191: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -191: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -191: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so -191: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so -191: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -191: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -191: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -191: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 17# 0x0000FFFF99BE4180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 18# 0x0000FFFF99BE4118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 19# 0x0000FFFF99BE40A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 20# 0x0000FFFF99BE4040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 21# 0x0000FFFF99BE3FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so -191: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so -191: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so -191: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so -191: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -191: 27# 0x0000FFFF9C36E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -191: 28# _PyObject_MakeTpCall in /usr/bin/python3 -191: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 -191: 30# 0x00000000004C3D1C in /usr/bin/python3 -191: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 -191: 32# _PyObject_Call_Prepend in /usr/bin/python3 -191: 33# 0x000000000052608C in /usr/bin/python3 -191: 34# _PyObject_MakeTpCall in /usr/bin/python3 -191: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 -191: 36# 0x00000000004C3D1C in /usr/bin/python3 -191: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 -191: 38# _PyObject_Call_Prepend in /usr/bin/python3 -191: 39# 0x000000000052608C in /usr/bin/python3 -191: 40# _PyObject_MakeTpCall in /usr/bin/python3 -191: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 -191: 42# 0x00000000004C3D1C in /usr/bin/python3 -191: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 -191: 44# _PyObject_Call_Prepend in /usr/bin/python3 -191: 45# 0x000000000052608C in /usr/bin/python3 -191: 46# _PyObject_MakeTpCall in /usr/bin/python3 -191: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 -191: 48# _PyObject_Call_Prepend in /usr/bin/python3 -191: 49# 0x000000000051FB4C in /usr/bin/python3 -191: 50# 0x000000000051B324 in /usr/bin/python3 -191: 51# _PyObject_MakeTpCall in /usr/bin/python3 -191: 52# _PyEval_EvalFrameDefault in /usr/bin/python3 -191: 53# PyEval_EvalCode in /usr/bin/python3 -191: 54# 0x0000000000595200 in /usr/bin/python3 -191: 55# 0x00000000006757AC in /usr/bin/python3 -191: 56# _PyRun_SimpleFileObject in /usr/bin/python3 -191: 57# _PyRun_AnyFileObject in /usr/bin/python3 -191: 58# Py_RunMain in /usr/bin/python3 -191: 59# Py_BytesMain in /usr/bin/python3 -191: 60# 0x0000FFFF9CCE229C in /lib/aarch64-linux-gnu/libc.so.6 -191: 61# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -191: 62# _start in /usr/bin/python3 -191: ---------- -191: **** -191: -182/230 Test #193: pyTestTrajectory ....................... Passed 0.85 sec -test 194 - Start 194: pyTestSGroups - -194: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/testSGroups.py" -194: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Wrap -194: Test timeout computed to be: 1500 -182: bulk, no symmetry -194: ............. -194: ---------------------------------------------------------------------- -194: Ran 13 tests in 0.054s -194: -194: OK -194: Testing SubstanceGroups wrapper -183/230 Test #194: pyTestSGroups .......................... Passed 0.76 sec +183/230 Test #193: pyTestTrajectory ....................... Passed 1.92 sec test 195 Start 195: pyTestThreads 195: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/testThreads.py" 195: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 195: Test timeout computed to be: 1500 -182: [02:23:35] Relabelling existing label -191: ....................[02:23:35] Explicit valence for atom # 1 F, 2, is greater than permitted -191: [02:23:35] Explicit valence for atom # 6 F, 2, is greater than permitted -191: [02:23:35] Can't kekulize mol. Unkekulized atoms: 3 4 5 -191: .................[02:23:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -182: Best mapping -184/230 Test #182: testRGroupDecomp ....................... Passed 8.76 sec +194: ............. +194: ---------------------------------------------------------------------- +194: Ran 13 tests in 0.066s +194: +194: OK +194: Testing SubstanceGroups wrapper +184/230 Test #194: pyTestSGroups .......................... Passed 1.22 sec test 196 Start 196: pyTestMultithreadedMolSupplier @@ -33666,71 +33685,224 @@ 196: Test timeout computed to be: 1500 196: .s. 196: ---------------------------------------------------------------------- -196: Ran 3 tests in 0.238s +196: Ran 3 tests in 0.277s 196: 196: OK (skipped=1) 196: Testing Smiles and SD MultithreadedMolSupplier -146: ... -146: ---------------------------------------------------------------------- -146: Ran 22 tests in 37.675s -146: -146: OK -185/230 Test #196: pyTestMultithreadedMolSupplier ......... Passed 0.56 sec +185/230 Test #196: pyTestMultithreadedMolSupplier ......... Passed 1.44 sec test 197 Start 197: pyTestPropertyLists 197: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/testPropertyLists.py" 197: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 197: Test timeout computed to be: 1500 -186/230 Test #146: pyDistGeomHelpers ...................... Passed 38.38 sec +191: ....................[23:10:58] Explicit valence for atom # 1 F, 2, is greater than permitted +191: [23:10:58] Explicit valence for atom # 6 F, 2, is greater than permitted +191: [23:10:58] Can't kekulize mol. Unkekulized atoms: 3 4 5 +191: .................[23:10:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +197: [23:10:58] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +197: [23:10:58] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +197: [23:10:58] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +197: .[23:10:58] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +197: [23:10:58] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +197: [23:10:58] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +197: ...[23:10:58] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +197: [23:10:58] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +197: [23:10:58] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +197: . +197: ---------------------------------------------------------------------- +197: Ran 5 tests in 0.028s +197: +197: OK +186/230 Test #197: pyTestPropertyLists .................... Passed 0.99 sec test 198 Start 198: pyCDXMLTest 198: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/Wrap/test_cdxml.py" 198: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 198: Test timeout computed to be: 1500 -197: [02:23:37] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -197: [02:23:37] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -197: [02:23:37] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -197: .[02:23:37] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -197: [02:23:37] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -197: [02:23:37] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -197: ...[02:23:37] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -197: [02:23:37] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -197: [02:23:37] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -197: . -197: ---------------------------------------------------------------------- -197: Ran 5 tests in 0.008s -197: -197: OK -187/230 Test #197: pyTestPropertyLists .................... Passed 0.41 sec +198: . +198: ---------------------------------------------------------------------- +198: Ran 1 test in 0.022s +198: +198: OK +187/230 Test #198: pyCDXMLTest ............................ Passed 1.28 sec test 199 Start 199: molStandardizeTest 199: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeTest 199: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 199: Test timeout computed to be: 1500 -198: . -198: ---------------------------------------------------------------------- -198: Ran 1 test in 0.015s -198: -198: OK -188/230 Test #198: pyCDXMLTest ............................ Passed 0.58 sec +181: ......[23:11:03] +181: +181: **** +181: Pre-condition Violation +181: RingInfo not initialized +181: Violation occurred on line 52 in file ./Code/GraphMol/RingInfo.cpp +181: Failed Expression: df_init +181: ---------- +181: Stacktrace: +181: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +181: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +181: 2# RDKit::RingInfo::numAtomRings(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +181: 3# RDKit::AtomRingQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 +181: 4# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +181: 5# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +181: 6# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +181: 7# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +181: 8# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +181: 9# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +181: 10# bool RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +181: 11# bool RDKit::HasSubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +181: 12# 0x0000FFFFB4094FD0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +181: 13# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +181: 14# 0x0000FFFFB66F15C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +181: 15# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +181: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +181: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +181: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +181: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +181: 20# 0x0000FFFFB3FF4180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +181: 21# 0x0000FFFFB3FF4118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +181: 22# 0x0000FFFFB3FF40A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +181: 23# 0x0000FFFFB3FF4040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +181: 24# 0x0000FFFFB3FF3FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +181: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so +181: 26# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so +181: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so +181: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so +181: 29# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +181: 30# 0x0000FFFFB66EE19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +181: 31# _PyObject_MakeTpCall in /usr/bin/python3 +181: 32# _PyEval_EvalFrameDefault in /usr/bin/python3 +181: 33# 0x00000000004C3D1C in /usr/bin/python3 +181: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 +181: 35# _PyObject_Call_Prepend in /usr/bin/python3 +181: 36# 0x000000000052608C in /usr/bin/python3 +181: 37# _PyObject_MakeTpCall in /usr/bin/python3 +181: 38# _PyEval_EvalFrameDefault in /usr/bin/python3 +181: 39# 0x00000000004C3D1C in /usr/bin/python3 +181: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 +181: 41# _PyObject_Call_Prepend in /usr/bin/python3 +181: 42# 0x000000000052608C in /usr/bin/python3 +181: 43# _PyObject_MakeTpCall in /usr/bin/python3 +181: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 +181: 45# 0x00000000004C3D1C in /usr/bin/python3 +181: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 +181: 47# _PyObject_Call_Prepend in /usr/bin/python3 +181: 48# 0x000000000052608C in /usr/bin/python3 +181: 49# _PyObject_MakeTpCall in /usr/bin/python3 +181: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 +181: 51# _PyObject_Call_Prepend in /usr/bin/python3 +181: 52# 0x000000000051FB4C in /usr/bin/python3 +181: 53# 0x000000000051B324 in /usr/bin/python3 +181: 54# _PyObject_MakeTpCall in /usr/bin/python3 +181: 55# _PyEval_EvalFrameDefault in /usr/bin/python3 +181: 56# PyEval_EvalCode in /usr/bin/python3 +181: 57# 0x0000000000595200 in /usr/bin/python3 +181: 58# 0x00000000006757AC in /usr/bin/python3 +181: 59# _PyRun_SimpleFileObject in /usr/bin/python3 +181: 60# _PyRun_AnyFileObject in /usr/bin/python3 +181: 61# Py_RunMain in /usr/bin/python3 +181: 62# Py_BytesMain in /usr/bin/python3 +181: 63# 0x0000FFFFB6ED229C in /lib/aarch64-linux-gnu/libc.so.6 +181: 64# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +181: 65# _start in /usr/bin/python3 +181: ---------- +181: **** +181: +181: [23:11:03] +181: +181: **** +181: Pre-condition Violation +181: RingInfo not initialized +181: Violation occurred on line 129 in file ./Code/GraphMol/RingInfo.cpp +181: Failed Expression: df_init +181: ---------- +181: Stacktrace: +181: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +181: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +181: 2# RDKit::RingInfo::numBondRings(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +181: 3# 0x0000FFFFB3B61748 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +181: 4# Queries::EqualityQuery::Match(RDKit::Bond const*) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +181: 5# RDKit::bondCompat(RDKit::Bond const*, RDKit::Bond const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +181: 6# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +181: 7# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +181: 8# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +181: 9# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +181: 10# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +181: 11# bool RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +181: 12# bool RDKit::HasSubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +181: 13# 0x0000FFFFB4094FD0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +181: 14# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +181: 15# 0x0000FFFFB66F15C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +181: 16# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +181: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +181: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +181: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +181: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +181: 21# 0x0000FFFFB3FF4180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +181: 22# 0x0000FFFFB3FF4118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +181: 23# 0x0000FFFFB3FF40A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +181: 24# 0x0000FFFFB3FF4040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +181: 25# 0x0000FFFFB3FF3FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +181: 26# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so +181: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so +181: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so +181: 29# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so +181: 30# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +181: 31# 0x0000FFFFB66EE19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +181: 32# _PyObject_MakeTpCall in /usr/bin/python3 +181: 33# _PyEval_EvalFrameDefault in /usr/bin/python3 +181: 34# 0x00000000004C3D1C in /usr/bin/python3 +181: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 +181: 36# _PyObject_Call_Prepend in /usr/bin/python3 +181: 37# 0x000000000052608C in /usr/bin/python3 +181: 38# _PyObject_MakeTpCall in /usr/bin/python3 +181: 39# _PyEval_EvalFrameDefault in /usr/bin/python3 +181: 40# 0x00000000004C3D1C in /usr/bin/python3 +181: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 +181: 42# _PyObject_Call_Prepend in /usr/bin/python3 +181: 43# 0x000000000052608C in /usr/bin/python3 +181: 44# _PyObject_MakeTpCall in /usr/bin/python3 +181: 45# _PyEval_EvalFrameDefault in /usr/bin/python3 +181: 46# 0x00000000004C3D1C in /usr/bin/python3 +181: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 +181: 48# _PyObject_Call_Prepend in /usr/bin/python3 +181: 49# 0x000000000052608C in /usr/bin/python3 +181: 50# _PyObject_MakeTpCall in /usr/bin/python3 +181: 51# _PyEval_EvalFrameDefault in /usr/bin/python3 +181: 52# _PyObject_Call_Prepend in /usr/bin/python3 +181: 53# 0x000000000051FB4C in /usr/bin/python3 +181: 54# 0x000000000051B324 in /usr/bin/python3 +181: 55# _PyObject_MakeTpCall in /usr/bin/python3 +181: 56# _PyEval_EvalFrameDefault in /usr/bin/python3 +181: 57# PyEval_EvalCode in /usr/bin/python3 +181: 58# 0x0000000000595200 in /usr/bin/python3 +181: 59# 0x00000000006757AC in /usr/bin/python3 +181: 60# _PyRun_SimpleFileObject in /usr/bin/python3 +181: 61# _PyRun_AnyFileObject in /usr/bin/python3 +181: 62# Py_RunMain in /usr/bin/python3 +181: 63# Py_BytesMain in /usr/bin/python3 +181: 64# 0x0000FFFFB6ED229C in /lib/aarch64-linux-gnu/libc.so.6 +181: 65# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +181: 66# _start in /usr/bin/python3 +181: ---------- +181: **** +181: +188/230 Test #199: molStandardizeTest ..................... Passed 3.19 sec test 200 Start 200: molNormalizeTest 200: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molNormalizeTest 200: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 200: Test timeout computed to be: 1500 -200: [02:23:37] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 -200: [02:23:37] Initializing Normalizer -200: [02:23:37] Running Normalizer -200: [02:23:37] Rule applied: BrokenazidetoN=N+=N- -200: [02:23:37] Initializing Normalizer -200: [02:23:37] Running Normalizer -200: [02:23:37] Initializing Normalizer -200: [02:23:37] Running Normalizer -189/230 Test #200: molNormalizeTest ....................... Passed 0.21 sec +200: [23:11:03] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 +148: --------------------------------- +148: test getO3AForProbeConfs +148: +148: *********************************************************** +189/230 Test #148: testO3AAlign ........................... Passed 64.53 sec test 201 Start 201: molValidateTest @@ -33755,21 +33927,28 @@ 201: ERROR: [StereoValidation] Bond 3 has assigned stereo type, but unexpected bond order. 201: there 201: ERROR: [StereoValidation] Atom 0 has stereo bonds, but less than 3 explicit substituents. -190/230 Test #201: molValidateTest ........................ Passed 0.08 sec +190/230 Test #201: molValidateTest ........................ Passed 0.13 sec test 202 Start 202: molChargeTest 202: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molChargeTest 202: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 202: Test timeout computed to be: 1500 -191/230 Test #202: molChargeTest .......................... Passed 0.12 sec +200: [23:11:04] Initializing Normalizer +200: [23:11:04] Running Normalizer +200: [23:11:04] Rule applied: BrokenazidetoN=N+=N- +200: [23:11:04] Initializing Normalizer +200: [23:11:04] Running Normalizer +200: [23:11:04] Initializing Normalizer +200: [23:11:04] Running Normalizer +191/230 Test #200: molNormalizeTest ....................... Passed 0.41 sec test 203 Start 203: molTautomerTest 203: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molTautomerTest 203: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 203: Test timeout computed to be: 1500 -192/230 Test #199: molStandardizeTest ..................... Passed 0.89 sec +192/230 Test #202: molChargeTest .......................... Passed 0.21 sec test 204 Start 204: molStandardizeSmallTest @@ -33783,131 +33962,31 @@ 205: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molFragmentTest 205: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 205: Test timeout computed to be: 1500 -205: [02:23:38] SMARTS Parse Error: syntax error while parsing: [Cl -205: [02:23:38] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' -194/230 Test #205: molFragmentTest ........................ Passed 0.12 sec +205: [23:11:04] SMARTS Parse Error: syntax error while parsing: [Cl +205: [23:11:04] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' +194/230 Test #205: molFragmentTest ........................ Passed 0.14 sec test 206 Start 206: molStandardizeCatchTest 206: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeCatchTest 206: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 206: Test timeout computed to be: 1500 -203: [02:23:38] Tautomer enumeration stopped at 292 tautomers: max transforms reached -206: Randomness seeded to: 4136603454 +206: Randomness seeded to: 1374203721 206: * - * - * - * m1 206: * - * - * - * m2 206: * - * - * - * m1 206: * - * - * - * m2 -206: [02:23:38] Can't kekulize mol. Unkekulized atoms: 3 7 -206: [02:23:39] Can't kekulize mol. Unkekulized atoms: 3 8 -206: [02:23:39] Can't kekulize mol. Unkekulized atoms: 2 3 4 -203: [02:23:39] Tautomer enumeration stopped at 292 tautomers: max transforms reached -203: [02:23:39] Tautomer enumeration stopped at 50 tautomers: max tautomers reached -203: [02:23:39] Tautomer enumeration stopped at 86 tautomers: canceled +206: [23:11:05] Can't kekulize mol. Unkekulized atoms: 3 7 +206: [23:11:05] Can't kekulize mol. Unkekulized atoms: 3 8 +206: [23:11:05] Can't kekulize mol. Unkekulized atoms: 2 3 4 +203: [23:11:05] Tautomer enumeration stopped at 292 tautomers: max transforms reached +203: [23:11:06] Tautomer enumeration stopped at 292 tautomers: max transforms reached +203: [23:11:06] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +203: [23:11:07] Tautomer enumeration stopped at 37 tautomers: canceled 203: Enumeration was canceled due to timeout (50 ms) -203: 375 -203: Enumeration has completed -203: [02:23:40] Tautomer enumeration stopped at 83 tautomers: canceled -203: CN=c1cc[nH]cn1 -203: CN=c1ccnc[nH]1 -203: CNc1ccncn1 -203: res: CNc1ccncn1 -203: CN=c1cccc[nH]1 -203: CNc1ccccn1 -203: res: CNc1ccccn1 -195/230 Test #203: molTautomerTest ........................ Passed 4.01 sec -test 207 - Start 207: molStandardizePipelineTest - -207: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizePipelineTest -207: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize -207: Test timeout computed to be: 1500 -207: Randomness seeded to: 3533279863 -207: 1 Counts line too short: '' on line4 -207: 1 Could not instantiate a valid molecule from input -207: 8 Molecule has no atoms -207: [02:23:42] Explicit valence for atom # 1 N, 4, is greater than permitted -207: [02:23:42] Explicit valence for atom # 1 N, 4, is greater than permitted -207: 8 Explicit valence for atom # 1 N, 4, is greater than permitted -207: 128 An error occurred while preparing the molecule for standardization. -207: 8 The molecule contains an unknown isotope: 3C -207: 4 Query atom 0 is not allowed -207: 4 Bond 0 of aromatic type is not allowed -207: 4 Bond 1 of aromatic type is not allowed -207: 4 Bond 2 of aromatic type is not allowed -207: 4 Bond 3 of aromatic type is not allowed -207: 4 Bond 5 of aromatic type is not allowed -207: 4 Bond 6 of aromatic type is not allowed -207: 4 Bond 2 of dative type is not allowed -207: 4 Bond 3 of dative type is not allowed -207: 4 Enhanced stereochemistry features are not allowed -207: 8 The radical at atom 0 is not allowed -207: [02:23:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -207: 16 The molecule includes non-null Z coordinates -207: 32 Atom 0 too close to bond 2 -207: 32 The length of bond 3 between atoms 0 and 3 exceeds a configured limit -207: 64 Atom 0 has 3 explicit substituents and multiple stereo bonds -207: 64 Atom 0 has adjacent stereo bonds with like orientation -207: [02:23:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -207: 16 The molecule includes non-null Z coordinates -207: 64 Atom 0 has adjacent stereo bonds with like orientation -207: 32 The length of bond 16 between atoms 16 and 1 exceeds a configured limit -207: 8388608 One or more metal atoms were disconnected. -207: 33554432 One or more disconnected fragments (e.g., counterions) were removed. -207: 67108864 The protonation state was adjusted. -207: 16777216 The representation of some functional groups was adjusted. -207: 67108864 The protonation state was adjusted. -207: 16777216 The representation of some functional groups was adjusted. -207: 67108864 The protonation state was adjusted. -207: 16777216 The representation of some functional groups was adjusted. -207: 16777216 The representation of some functional groups was adjusted. -207: 67108864 The protonation state was adjusted. -207: 16777216 The representation of some functional groups was adjusted. -207: 67108864 The protonation state was adjusted. -207: 16777216 The representation of some functional groups was adjusted. -207: 67108864 The protonation state was adjusted. -207: 16777216 The representation of some functional groups was adjusted. -207: 67108864 The protonation state was adjusted. -207: 8388608 One or more metal atoms were disconnected. -207: 33554432 One or more disconnected fragments (e.g., counterions) were removed. -207: 67108864 The protonation state was adjusted. -207: 8388608 One or more metal atoms were disconnected. -207: 33554432 One or more disconnected fragments (e.g., counterions) were removed. -207: 67108864 The protonation state was adjusted. -207: 8388608 One or more metal atoms were disconnected. -207: 33554432 One or more disconnected fragments (e.g., counterions) were removed. -207: 67108864 The protonation state was adjusted. -207: 8388608 One or more metal atoms were disconnected. -207: 33554432 One or more disconnected fragments (e.g., counterions) were removed. -207: 67108864 The protonation state was adjusted. -207: 8388608 One or more metal atoms were disconnected. -207: 33554432 One or more disconnected fragments (e.g., counterions) were removed. -207: 67108864 The protonation state was adjusted. -207: 16777216 The "wavy" style of bond 4 was removed -207: 16777216 Double bond 1 was assigned an undefined/unknown stereochemical configuration -207: 16777216 The "wavy" style of bond 2 was removed -207: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration -207: 16777216 The "wavy" style of bond 1 was removed -207: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration -207: 16777216 The "wavy" style of bond 1 was removed -207: 16777216 The "wavy" style of bond 4 was removed -207: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration -207: 16777216 The "wavy" style of bond 3 was removed -207: 16777216 The representation of some functional groups was adjusted. -207: [02:23:42] Can't kekulize mol. Unkekulized atoms: 2 3 5 -191: ..[02:23:42] +191: ..[23:11:07] 191: 191: **** -207: =============================================================================== -207: All tests passed (268 assertions in 5 test cases) -207: -196/230 Test #207: molStandardizePipelineTest ............. Passed 0.31 sec -test 208 - Start 208: pyMolStandardize - -208: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/Wrap/testMolStandardize.py" -208: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap -208: Test timeout computed to be: 1500 191: Pre-condition Violation 191: no owner 191: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h @@ -33919,7 +33998,7 @@ 191: 2# RDKit::Atom::getOwningMol() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 191: 3# boost::python::objects::caller_py_function_impl, boost::mpl::vector2 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 191: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -191: 5# 0x0000FFFF9C3715C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +191: 5# 0x0000FFFF933215C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 191: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 191: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 191: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -33930,17 +34009,17 @@ 191: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 191: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 16# 0x0000FFFF99BE4180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 17# 0x0000FFFF99BE4118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 18# 0x0000FFFF99BE40A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 19# 0x0000FFFF99BE4040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 20# 0x0000FFFF99BE3FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 16# 0x0000FFFF90B94180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 17# 0x0000FFFF90B94118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 18# 0x0000FFFF90B940A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 19# 0x0000FFFF90B94040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 20# 0x0000FFFF90B93FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 191: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -191: 26# 0x0000FFFF9C36E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +191: 26# 0x0000FFFF9331E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 191: 27# _PyObject_MakeTpCall in /usr/bin/python3 191: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 29# 0x00000000004C3D1C in /usr/bin/python3 @@ -33973,13 +34052,13 @@ 191: 56# _PyRun_AnyFileObject in /usr/bin/python3 191: 57# Py_RunMain in /usr/bin/python3 191: 58# Py_BytesMain in /usr/bin/python3 -191: 59# 0x0000FFFF9CCE229C in /lib/aarch64-linux-gnu/libc.so.6 +191: 59# 0x0000FFFF93C9229C in /lib/aarch64-linux-gnu/libc.so.6 191: 60# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 191: 61# _start in /usr/bin/python3 191: ---------- 191: **** 191: -191: [02:23:42] +191: [23:11:07] 191: 191: **** 191: Pre-condition Violation @@ -33994,7 +34073,7 @@ 191: 3# RDKit::AtomGetNeighbors(RDKit::Atom*) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 191: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 191: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -191: 6# 0x0000FFFF9C3715C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +191: 6# 0x0000FFFF933215C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 191: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 191: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 191: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34005,17 +34084,17 @@ 191: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 191: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 17# 0x0000FFFF99BE4180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 18# 0x0000FFFF99BE4118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 19# 0x0000FFFF99BE40A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 20# 0x0000FFFF99BE4040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 21# 0x0000FFFF99BE3FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 17# 0x0000FFFF90B94180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 18# 0x0000FFFF90B94118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 19# 0x0000FFFF90B940A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 20# 0x0000FFFF90B94040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 21# 0x0000FFFF90B93FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 191: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -191: 27# 0x0000FFFF9C36E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +191: 27# 0x0000FFFF9331E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 191: 28# _PyObject_MakeTpCall in /usr/bin/python3 191: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 30# 0x00000000004C3D1C in /usr/bin/python3 @@ -34048,13 +34127,13 @@ 191: 57# _PyRun_AnyFileObject in /usr/bin/python3 191: 58# Py_RunMain in /usr/bin/python3 191: 59# Py_BytesMain in /usr/bin/python3 -191: 60# 0x0000FFFF9CCE229C in /lib/aarch64-linux-gnu/libc.so.6 +191: 60# 0x0000FFFF93C9229C in /lib/aarch64-linux-gnu/libc.so.6 191: 61# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 191: 62# _start in /usr/bin/python3 191: ---------- 191: **** 191: -191: [02:23:42] +191: [23:11:07] 191: 191: **** 191: Pre-condition Violation @@ -34069,7 +34148,7 @@ 191: 3# RDKit::AtomGetBonds(RDKit::Atom*) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 191: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 191: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -191: 6# 0x0000FFFF9C3715C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +191: 6# 0x0000FFFF933215C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 191: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 191: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 191: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34080,17 +34159,17 @@ 191: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 191: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 17# 0x0000FFFF99BE4180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 18# 0x0000FFFF99BE4118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 19# 0x0000FFFF99BE40A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 20# 0x0000FFFF99BE4040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 21# 0x0000FFFF99BE3FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 17# 0x0000FFFF90B94180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 18# 0x0000FFFF90B94118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 19# 0x0000FFFF90B940A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 20# 0x0000FFFF90B94040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 21# 0x0000FFFF90B93FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 191: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -191: 27# 0x0000FFFF9C36E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +191: 27# 0x0000FFFF9331E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 191: 28# _PyObject_MakeTpCall in /usr/bin/python3 191: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 30# 0x00000000004C3D1C in /usr/bin/python3 @@ -34123,13 +34202,13 @@ 191: 57# _PyRun_AnyFileObject in /usr/bin/python3 191: 58# Py_RunMain in /usr/bin/python3 191: 59# Py_BytesMain in /usr/bin/python3 -191: 60# 0x0000FFFF9CCE229C in /lib/aarch64-linux-gnu/libc.so.6 +191: 60# 0x0000FFFF93C9229C in /lib/aarch64-linux-gnu/libc.so.6 191: 61# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 191: 62# _start in /usr/bin/python3 191: ---------- 191: **** 191: -191: [02:23:42] +191: [23:11:07] 191: 191: **** 191: Pre-condition Violation @@ -34144,7 +34223,7 @@ 191: 3# RDKit::AtomIsInRing(RDKit::Atom const*) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 191: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 191: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -191: 6# 0x0000FFFF9C3715C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +191: 6# 0x0000FFFF933215C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 191: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 191: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 191: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34155,17 +34234,17 @@ 191: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 191: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 17# 0x0000FFFF99BE4180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 18# 0x0000FFFF99BE4118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 19# 0x0000FFFF99BE40A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 20# 0x0000FFFF99BE4040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 21# 0x0000FFFF99BE3FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 17# 0x0000FFFF90B94180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 18# 0x0000FFFF90B94118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 19# 0x0000FFFF90B940A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 20# 0x0000FFFF90B94040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 21# 0x0000FFFF90B93FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 191: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -191: 27# 0x0000FFFF9C36E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +191: 27# 0x0000FFFF9331E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 191: 28# _PyObject_MakeTpCall in /usr/bin/python3 191: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 30# 0x00000000004C3D1C in /usr/bin/python3 @@ -34198,13 +34277,13 @@ 191: 57# _PyRun_AnyFileObject in /usr/bin/python3 191: 58# Py_RunMain in /usr/bin/python3 191: 59# Py_BytesMain in /usr/bin/python3 -191: 60# 0x0000FFFF9CCE229C in /lib/aarch64-linux-gnu/libc.so.6 +191: 60# 0x0000FFFF93C9229C in /lib/aarch64-linux-gnu/libc.so.6 191: 61# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 191: 62# _start in /usr/bin/python3 191: ---------- 191: **** 191: -191: [02:23:42] +191: [23:11:07] 191: 191: **** 191: Pre-condition Violation @@ -34219,7 +34298,7 @@ 191: 3# RDKit::AtomIsInRingSize(RDKit::Atom const*, int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 191: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 191: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -191: 6# 0x0000FFFF9C3715C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +191: 6# 0x0000FFFF933215C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 191: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 191: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 191: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34230,17 +34309,17 @@ 191: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 191: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 17# 0x0000FFFF99BE4180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 18# 0x0000FFFF99BE4118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 19# 0x0000FFFF99BE40A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 20# 0x0000FFFF99BE4040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 21# 0x0000FFFF99BE3FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 17# 0x0000FFFF90B94180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 18# 0x0000FFFF90B94118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 19# 0x0000FFFF90B940A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 20# 0x0000FFFF90B94040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 21# 0x0000FFFF90B93FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 191: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -191: 27# 0x0000FFFF9C36E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +191: 27# 0x0000FFFF9331E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 191: 28# _PyObject_MakeTpCall in /usr/bin/python3 191: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 30# 0x00000000004C3D1C in /usr/bin/python3 @@ -34273,13 +34352,13 @@ 191: 57# _PyRun_AnyFileObject in /usr/bin/python3 191: 58# Py_RunMain in /usr/bin/python3 191: 59# Py_BytesMain in /usr/bin/python3 -191: 60# 0x0000FFFF9CCE229C in /lib/aarch64-linux-gnu/libc.so.6 +191: 60# 0x0000FFFF93C9229C in /lib/aarch64-linux-gnu/libc.so.6 191: 61# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 191: 62# _start in /usr/bin/python3 191: ---------- 191: **** 191: -191: .....[02:23:42] +191: .....[23:11:07] 191: 191: **** 191: Range Error @@ -34293,7 +34372,7 @@ 191: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 191: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 191: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -191: 5# 0x0000FFFF9C3715C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +191: 5# 0x0000FFFF933215C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 191: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 191: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 191: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34304,17 +34383,17 @@ 191: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 191: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 16# 0x0000FFFF99BE4180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 17# 0x0000FFFF99BE4118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 18# 0x0000FFFF99BE40A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 19# 0x0000FFFF99BE4040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 20# 0x0000FFFF99BE3FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 16# 0x0000FFFF90B94180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 17# 0x0000FFFF90B94118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 18# 0x0000FFFF90B940A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 19# 0x0000FFFF90B94040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 20# 0x0000FFFF90B93FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 191: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -191: 26# 0x0000FFFF9C36E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +191: 26# 0x0000FFFF9331E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 191: 27# _PyObject_MakeTpCall in /usr/bin/python3 191: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 29# 0x00000000004C3D1C in /usr/bin/python3 @@ -34347,41 +34426,41 @@ 191: 56# _PyRun_AnyFileObject in /usr/bin/python3 191: 57# Py_RunMain in /usr/bin/python3 191: 58# Py_BytesMain in /usr/bin/python3 -191: 59# 0x0000FFFF9CCE229C in /lib/aarch64-linux-gnu/libc.so.6 +191: 59# 0x0000FFFF93C9229C in /lib/aarch64-linux-gnu/libc.so.6 191: 60# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 191: 61# _start in /usr/bin/python3 191: ---------- 191: **** 191: -191: ......[02:23:42] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -191: [02:23:42] ERROR: Smiles parse error on line 0 -191: [02:23:42] ERROR: Cannot create molecule from : 'c1ccccc' -191: [02:23:42] SMILES Parse Error: extra open parentheses for input: 'C(C' -191: [02:23:42] ERROR: Smiles parse error on line 3 -191: [02:23:42] ERROR: Cannot create molecule from : 'C(C' -191: [02:23:42] Explicit valence for atom # 1 C, 5, is greater than permitted -191: [02:23:42] ERROR: Could not sanitize molecule on line 6 -191: [02:23:42] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -191: [02:23:42] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -191: [02:23:42] ERROR: Smiles parse error on line 0 -191: [02:23:42] ERROR: Cannot create molecule from : 'c1ccccc' -191: [02:23:42] SMILES Parse Error: extra open parentheses for input: 'C(C' -191: [02:23:42] ERROR: Smiles parse error on line 3 -191: [02:23:42] ERROR: Cannot create molecule from : 'C(C' -191: [02:23:42] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' -191: [02:23:42] ERROR: Smiles parse error on line 6 -191: [02:23:42] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' -191: [02:23:42] Explicit valence for atom # 1 F, 2, is greater than permitted -191: [02:23:42] ERROR: Could not sanitize molecule ending on line 21 -191: [02:23:42] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -191: [02:23:42] ERROR: EOF hit while reading atoms -191: [02:23:42] ERROR: moving to the beginning of the next molecule -191: [02:23:42] Explicit valence for atom # 1 F, 2, is greater than permitted -191: [02:23:42] ERROR: Could not sanitize molecule ending on line 21 -191: [02:23:42] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -191: [02:23:42] ERROR: EOF hit while reading atoms -191: [02:23:42] ERROR: moving to the beginning of the next molecule -191: ....[02:23:42] +191: ......[23:11:08] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +191: [23:11:08] ERROR: Smiles parse error on line 0 +191: [23:11:08] ERROR: Cannot create molecule from : 'c1ccccc' +191: [23:11:08] SMILES Parse Error: extra open parentheses for input: 'C(C' +191: [23:11:08] ERROR: Smiles parse error on line 3 +191: [23:11:08] ERROR: Cannot create molecule from : 'C(C' +191: [23:11:08] Explicit valence for atom # 1 C, 5, is greater than permitted +191: [23:11:08] ERROR: Could not sanitize molecule on line 6 +191: [23:11:08] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +191: [23:11:08] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +191: [23:11:08] ERROR: Smiles parse error on line 0 +191: [23:11:08] ERROR: Cannot create molecule from : 'c1ccccc' +191: [23:11:08] SMILES Parse Error: extra open parentheses for input: 'C(C' +191: [23:11:08] ERROR: Smiles parse error on line 3 +191: [23:11:08] ERROR: Cannot create molecule from : 'C(C' +191: [23:11:08] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' +191: [23:11:08] ERROR: Smiles parse error on line 6 +191: [23:11:08] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' +191: [23:11:08] Explicit valence for atom # 1 F, 2, is greater than permitted +191: [23:11:08] ERROR: Could not sanitize molecule ending on line 21 +191: [23:11:08] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +191: [23:11:08] ERROR: EOF hit while reading atoms +191: [23:11:08] ERROR: moving to the beginning of the next molecule +191: [23:11:08] Explicit valence for atom # 1 F, 2, is greater than permitted +191: [23:11:08] ERROR: Could not sanitize molecule ending on line 21 +191: [23:11:08] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +191: [23:11:08] ERROR: EOF hit while reading atoms +191: [23:11:08] ERROR: moving to the beginning of the next molecule +191: ....[23:11:08] 191: 191: **** 191: Pre-condition Violation @@ -34395,7 +34474,7 @@ 191: 2# RDKit::RingInfo::numRings() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 191: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 191: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -191: 5# 0x0000FFFF9C3715C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +191: 5# 0x0000FFFF933215C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 191: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 191: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 191: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34406,17 +34485,17 @@ 191: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 191: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 16# 0x0000FFFF99BE4180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 17# 0x0000FFFF99BE4118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 18# 0x0000FFFF99BE40A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 19# 0x0000FFFF99BE4040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 20# 0x0000FFFF99BE3FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 16# 0x0000FFFF90B94180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 17# 0x0000FFFF90B94118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 18# 0x0000FFFF90B940A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 19# 0x0000FFFF90B94040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 20# 0x0000FFFF90B93FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 191: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -191: 26# 0x0000FFFF9C36E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +191: 26# 0x0000FFFF9331E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 191: 27# _PyObject_MakeTpCall in /usr/bin/python3 191: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 29# 0x00000000004C3D1C in /usr/bin/python3 @@ -34449,13 +34528,13 @@ 191: 56# _PyRun_AnyFileObject in /usr/bin/python3 191: 57# Py_RunMain in /usr/bin/python3 191: 58# Py_BytesMain in /usr/bin/python3 -191: 59# 0x0000FFFF9CCE229C in /lib/aarch64-linux-gnu/libc.so.6 +191: 59# 0x0000FFFF93C9229C in /lib/aarch64-linux-gnu/libc.so.6 191: 60# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 191: 61# _start in /usr/bin/python3 191: ---------- 191: **** 191: -191: ............[02:23:42] +191: ............[23:11:08] 191: 191: **** 191: Range Error @@ -34469,7 +34548,7 @@ 191: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 191: 3# boost::python::objects::caller_py_function_impl >, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 191: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -191: 5# 0x0000FFFF9C3715C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +191: 5# 0x0000FFFF933215C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 191: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 191: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 191: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34480,17 +34559,17 @@ 191: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 191: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 191: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 16# 0x0000FFFF99BE4180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 17# 0x0000FFFF99BE4118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 18# 0x0000FFFF99BE40A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 19# 0x0000FFFF99BE4040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -191: 20# 0x0000FFFF99BE3FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 16# 0x0000FFFF90B94180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 17# 0x0000FFFF90B94118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 18# 0x0000FFFF90B940A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 19# 0x0000FFFF90B94040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +191: 20# 0x0000FFFF90B93FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 191: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 191: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -191: 26# 0x0000FFFF9C36E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +191: 26# 0x0000FFFF9331E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 191: 27# _PyObject_MakeTpCall in /usr/bin/python3 191: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 191: 29# 0x00000000004C3D1C in /usr/bin/python3 @@ -34523,233 +34602,179 @@ 191: 56# _PyRun_AnyFileObject in /usr/bin/python3 191: 57# Py_RunMain in /usr/bin/python3 191: 58# Py_BytesMain in /usr/bin/python3 -191: 59# 0x0000FFFF9CCE229C in /lib/aarch64-linux-gnu/libc.so.6 +191: 59# 0x0000FFFF93C9229C in /lib/aarch64-linux-gnu/libc.so.6 191: 60# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 191: 61# _start in /usr/bin/python3 191: ---------- 191: **** 191: -191: ...[02:23:42] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -191: ............................[02:23:42] SMILES Parse Error: unclosed ring for input: 'C1CC' +191: ...[23:11:08] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +203: 375 +203: Enumeration has completed +203: [23:11:08] Tautomer enumeration stopped at 33 tautomers: canceled +191: ............................[23:11:08] SMILES Parse Error: unclosed ring for input: 'C1CC' 191: ......smi: CC1=C(n2cccc2[C@H](C)Cl)C(C)CCC1 |(2.679,0.4142,;1.3509,1.181,;0.0229,0.4141,;0.0229,-1.1195,;1.2645,-2.0302,;0.7901,-3.4813,;-0.7446,-3.4813,;-1.219,-2.0302,;-2.679,-1.5609,;-3.0039,-0.0556,;-3.8202,-2.595,;-1.3054,1.1809,;-2.6335,0.4141,;-1.3054,2.7145,;0.0229,3.4813,;1.3509,2.7146,),wD:8.9,2.11,a:2,&1:8| -191: 643 -191: ..[02:23:42] WARNING: not removing hydrogen atom without neighbors -191: [02:23:42] WARNING: not removing hydrogen atom with dummy atom neighbors -191: [02:23:42] WARNING: not removing hydrogen atom with wedged bond -191: [02:23:42] WARNING: not removing hydrogen atom without neighbors -191: [02:23:42] WARNING: not removing hydrogen atom with dummy atom neighbors -191: ......[02:23:42] Explicit valence for atom # 1 F, 2, is greater than permitted -191: [02:23:42] Can't kekulize mol. Unkekulized atoms: 0 1 2 -191: .[02:23:42] Explicit valence for atom # 1 F, 2, is greater than permitted -191: [02:23:42] Explicit valence for atom # 1 F, 2, is greater than permitted -191: [02:23:42] Explicit valence for atom # 1 F, 2, is greater than permitted -191: [02:23:42] Explicit valence for atom # 1 F, 2, is greater than permitted -191: [02:23:42] Can't kekulize mol. Unkekulized atoms: 0 1 2 -191: [02:23:42] Can't kekulize mol. Unkekulized atoms: 0 1 2 -191: [02:23:42] Can't kekulize mol. Unkekulized atoms: 0 1 2 -191: ..........[02:23:43] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -191: [02:23:43] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -191: .[02:23:43] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -191: [02:23:43] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -191: ..[02:23:43] SMILES Parse Error: syntax error while parsing: error -191: [02:23:43] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' -191: [02:23:43] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' -191: [02:23:43] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' -191: [02:23:43] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' -191: .........................[02:23:43] SMILES Parse Error: syntax error while parsing: garbage_0 -191: [02:23:43] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' -191: [02:23:43] SMILES Parse Error: syntax error while parsing: garbage_2 -191: [02:23:43] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' -191: [02:23:43] SMILES Parse Error: syntax error while parsing: garbage_4 -191: [02:23:43] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' +191: 279 +191: ..[23:11:08] WARNING: not removing hydrogen atom without neighbors +191: [23:11:08] WARNING: not removing hydrogen atom with dummy atom neighbors +191: [23:11:08] WARNING: not removing hydrogen atom with wedged bond +191: [23:11:08] WARNING: not removing hydrogen atom without neighbors +191: [23:11:08] WARNING: not removing hydrogen atom with dummy atom neighbors +191: ......[23:11:09] Explicit valence for atom # 1 F, 2, is greater than permitted +191: [23:11:09] Can't kekulize mol. Unkekulized atoms: 0 1 2 +191: .[23:11:09] Explicit valence for atom # 1 F, 2, is greater than permitted +191: [23:11:09] Explicit valence for atom # 1 F, 2, is greater than permitted +191: [23:11:09] Explicit valence for atom # 1 F, 2, is greater than permitted +191: [23:11:09] Explicit valence for atom # 1 F, 2, is greater than permitted +191: [23:11:09] Can't kekulize mol. Unkekulized atoms: 0 1 2 +191: [23:11:09] Can't kekulize mol. Unkekulized atoms: 0 1 2 +191: [23:11:09] Can't kekulize mol. Unkekulized atoms: 0 1 2 +191: ..........[23:11:09] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +191: [23:11:09] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +191: .[23:11:09] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +191: [23:11:09] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +191: ..[23:11:09] SMILES Parse Error: syntax error while parsing: error +191: [23:11:09] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' +191: [23:11:09] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' +191: [23:11:09] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' +191: [23:11:09] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' +191: .........................[23:11:09] SMILES Parse Error: syntax error while parsing: garbage_0 +191: [23:11:09] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' +191: [23:11:09] SMILES Parse Error: syntax error while parsing: garbage_2 +191: [23:11:09] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' +191: [23:11:09] SMILES Parse Error: syntax error while parsing: garbage_4 +191: [23:11:09] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' 191: ........... 191: ---------------------------------------------------------------------- -191: Ran 277 tests in 9.837s +191: Ran 277 tests in 15.598s 191: 191: OK 191: supplier: 191: supplier: 191: supplier: -197/230 Test #191: pyGraphMolWrap ......................... Passed 10.60 sec +145: [23:11:09] UFFTYPER: Unrecognized atom type: S_6+6 (0) +145: [23:11:09] UFFTYPER: Warning: hybridization set to SP3 for atom 0 +145: [23:11:09] UFFTYPER: Unrecognized charge state for atom: 0 +195/230 Test #191: pyGraphMolWrap ......................... Passed 17.50 sec +test 207 + Start 207: molStandardizePipelineTest + +207: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizePipelineTest +207: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize +207: Test timeout computed to be: 1500 +207: Randomness seeded to: 4075057577 +207: 1 Counts line too short: '' on line4 +207: 1 Could not instantiate a valid molecule from input +207: 8 Molecule has no atoms +207: [23:11:09] Explicit valence for atom # 1 N, 4, is greater than permitted +207: [23:11:09] Explicit valence for atom # 1 N, 4, is greater than permitted +207: 8 Explicit valence for atom # 1 N, 4, is greater than permitted +207: 128 An error occurred while preparing the molecule for standardization. +207: 8 The molecule contains an unknown isotope: 3C +207: 4 Query atom 0 is not allowed +207: 4 Bond 0 of aromatic type is not allowed +207: 4 Bond 1 of aromatic type is not allowed +207: 4 Bond 2 of aromatic type is not allowed +207: 4 Bond 3 of aromatic type is not allowed +207: 4 Bond 5 of aromatic type is not allowed +207: 4 Bond 6 of aromatic type is not allowed +207: 4 Bond 2 of dative type is not allowed +207: 4 Bond 3 of dative type is not allowed +207: 4 Enhanced stereochemistry features are not allowed +207: 8 The radical at atom 0 is not allowed +207: [23:11:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +207: 16 The molecule includes non-null Z coordinates +207: 32 Atom 0 too close to bond 2 +207: 32 The length of bond 3 between atoms 0 and 3 exceeds a configured limit +207: 64 Atom 0 has 3 explicit substituents and multiple stereo bonds +207: 64 Atom 0 has adjacent stereo bonds with like orientation +207: [23:11:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +207: 16 The molecule includes non-null Z coordinates +207: 64 Atom 0 has adjacent stereo bonds with like orientation +203: CN=c1cc[nH]cn1 +203: CN=c1ccnc[nH]1 +203: CNc1ccncn1 +203: res: CNc1ccncn1 +203: CN=c1cccc[nH]1 +203: CNc1ccccn1 +203: res: CNc1ccccn1 +207: 32 The length of bond 16 between atoms 16 and 1 exceeds a configured limit +207: 8388608 One or more metal atoms were disconnected. +207: 33554432 One or more disconnected fragments (e.g., counterions) were removed. +207: 67108864 The protonation state was adjusted. +207: 16777216 The representation of some functional groups was adjusted. +207: 67108864 The protonation state was adjusted. +207: 16777216 The representation of some functional groups was adjusted. +207: 67108864 The protonation state was adjusted. +207: 16777216 The representation of some functional groups was adjusted. +207: 16777216 The representation of some functional groups was adjusted. +207: 67108864 The protonation state was adjusted. +207: 16777216 The representation of some functional groups was adjusted. +207: 67108864 The protonation state was adjusted. +207: 16777216 The representation of some functional groups was adjusted. +207: 67108864 The protonation state was adjusted. +207: 16777216 The representation of some functional groups was adjusted. +207: 67108864 The protonation state was adjusted. +207: 8388608 One or more metal atoms were disconnected. +207: 33554432 One or more disconnected fragments (e.g., counterions) were removed. +207: 67108864 The protonation state was adjusted. +207: 8388608 One or more metal atoms were disconnected. +207: 33554432 One or more disconnected fragments (e.g., counterions) were removed. +207: 67108864 The protonation state was adjusted. +207: 8388608 One or more metal atoms were disconnected. +207: 33554432 One or more disconnected fragments (e.g., counterions) were removed. +207: 67108864 The protonation state was adjusted. +207: 8388608 One or more metal atoms were disconnected. +207: 33554432 One or more disconnected fragments (e.g., counterions) were removed. +207: 67108864 The protonation state was adjusted. +207: 8388608 One or more metal atoms were disconnected. +207: 33554432 One or more disconnected fragments (e.g., counterions) were removed. +207: 67108864 The protonation state was adjusted. +207: 16777216 The "wavy" style of bond 4 was removed +207: 16777216 Double bond 1 was assigned an undefined/unknown stereochemical configuration +207: 16777216 The "wavy" style of bond 2 was removed +207: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration +207: 16777216 The "wavy" style of bond 1 was removed +207: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration +207: 16777216 The "wavy" style of bond 1 was removed +207: 16777216 The "wavy" style of bond 4 was removed +207: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration +207: 16777216 The "wavy" style of bond 3 was removed +207: 16777216 The representation of some functional groups was adjusted. +207: [23:11:10] Can't kekulize mol. Unkekulized atoms: 2 3 5 +207: =============================================================================== +207: All tests passed (268 assertions in 5 test cases) +207: +196/230 Test #207: molStandardizePipelineTest ............. Passed 0.43 sec +test 208 + Start 208: pyMolStandardize + +208: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolStandardize/Wrap/testMolStandardize.py" +208: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap +208: Test timeout computed to be: 1500 +197/230 Test #203: molTautomerTest ........................ Passed 6.47 sec test 209 Start 209: testScaffoldNetwork 209: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/testScaffoldNetwork 209: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork 209: Test timeout computed to be: 1500 -208: .....[02:23:44] Tautomer enumeration stopped at 292 tautomers: max transforms reached -208: [02:23:44] Tautomer enumeration stopped at 50 tautomers: max tautomers reached -208: .[02:23:44] Tautomer enumeration stopped at 31 tautomers: canceled +208: .....[23:11:11] Tautomer enumeration stopped at 292 tautomers: max transforms reached +208: [23:11:12] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +208: .[23:11:12] Tautomer enumeration stopped at 32 tautomers: canceled 208: Enumeration was canceled due to timeout (50 ms) -181: ......[02:23:44] -181: -181: **** -181: Pre-condition Violation -181: RingInfo not initialized -181: Violation occurred on line 52 in file ./Code/GraphMol/RingInfo.cpp -181: Failed Expression: df_init -181: ---------- -181: Stacktrace: -181: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -181: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -181: 2# RDKit::RingInfo::numAtomRings(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -181: 3# RDKit::AtomRingQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 -181: 4# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -181: 5# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -181: 6# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -181: 7# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -181: 8# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -181: 9# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -181: 10# bool RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -181: 11# bool RDKit::HasSubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -181: 12# 0x0000FFFF8C674FD0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -181: 13# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -181: 14# 0x0000FFFF8ECD15C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -181: 15# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -181: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -181: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -181: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -181: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -181: 20# 0x0000FFFF8C5D4180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -181: 21# 0x0000FFFF8C5D4118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -181: 22# 0x0000FFFF8C5D40A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -181: 23# 0x0000FFFF8C5D4040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -181: 24# 0x0000FFFF8C5D3FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -181: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so -181: 26# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so -181: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so -181: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so -181: 29# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -181: 30# 0x0000FFFF8ECCE19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -181: 31# _PyObject_MakeTpCall in /usr/bin/python3 -181: 32# _PyEval_EvalFrameDefault in /usr/bin/python3 -181: 33# 0x00000000004C3D1C in /usr/bin/python3 -181: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 -181: 35# _PyObject_Call_Prepend in /usr/bin/python3 -181: 36# 0x000000000052608C in /usr/bin/python3 -181: 37# _PyObject_MakeTpCall in /usr/bin/python3 -181: 38# _PyEval_EvalFrameDefault in /usr/bin/python3 -181: 39# 0x00000000004C3D1C in /usr/bin/python3 -181: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 -181: 41# _PyObject_Call_Prepend in /usr/bin/python3 -181: 42# 0x000000000052608C in /usr/bin/python3 -181: 43# _PyObject_MakeTpCall in /usr/bin/python3 -181: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 -181: 45# 0x00000000004C3D1C in /usr/bin/python3 -181: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 -181: 47# _PyObject_Call_Prepend in /usr/bin/python3 -181: 48# 0x000000000052608C in /usr/bin/python3 -181: 49# _PyObject_MakeTpCall in /usr/bin/python3 -181: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 -181: 51# _PyObject_Call_Prepend in /usr/bin/python3 -181: 52# 0x000000000051FB4C in /usr/bin/python3 -181: 53# 0x000000000051B324 in /usr/bin/python3 -181: 54# _PyObject_MakeTpCall in /usr/bin/python3 -181: 55# _PyEval_EvalFrameDefault in /usr/bin/python3 -181: 56# PyEval_EvalCode in /usr/bin/python3 -181: 57# 0x0000000000595200 in /usr/bin/python3 -181: 58# 0x00000000006757AC in /usr/bin/python3 -181: 59# _PyRun_SimpleFileObject in /usr/bin/python3 -181: 60# _PyRun_AnyFileObject in /usr/bin/python3 -181: 61# Py_RunMain in /usr/bin/python3 -181: 62# Py_BytesMain in /usr/bin/python3 -181: 63# 0x0000FFFF8F4B229C in /lib/aarch64-linux-gnu/libc.so.6 -181: 64# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -181: 65# _start in /usr/bin/python3 -181: ---------- -181: **** -181: -181: [02:23:44] -181: -181: **** -181: Pre-condition Violation -181: RingInfo not initialized -181: Violation occurred on line 129 in file ./Code/GraphMol/RingInfo.cpp -181: Failed Expression: df_init -181: ---------- -181: Stacktrace: -181: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -181: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -181: 2# RDKit::RingInfo::numBondRings(unsigned int) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -181: 3# 0x0000FFFF8C141748 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -181: 4# Queries::EqualityQuery::Match(RDKit::Bond const*) const in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -181: 5# RDKit::bondCompat(RDKit::Bond const*, RDKit::Bond const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -181: 6# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -181: 7# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -181: 8# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -181: 9# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -181: 10# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -181: 11# bool RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -181: 12# bool RDKit::HasSubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -181: 13# 0x0000FFFF8C674FD0 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -181: 14# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -181: 15# 0x0000FFFF8ECD15C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -181: 16# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -181: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -181: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -181: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -181: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -181: 21# 0x0000FFFF8C5D4180 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -181: 22# 0x0000FFFF8C5D4118 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -181: 23# 0x0000FFFF8C5D40A8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -181: 24# 0x0000FFFF8C5D4040 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -181: 25# 0x0000FFFF8C5D3FD8 in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -181: 26# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so -181: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so -181: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so -181: 29# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so -181: 30# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -181: 31# 0x0000FFFF8ECCE19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -181: 32# _PyObject_MakeTpCall in /usr/bin/python3 -181: 33# _PyEval_EvalFrameDefault in /usr/bin/python3 -181: 34# 0x00000000004C3D1C in /usr/bin/python3 -181: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 -181: 36# _PyObject_Call_Prepend in /usr/bin/python3 -181: 37# 0x000000000052608C in /usr/bin/python3 -181: 38# _PyObject_MakeTpCall in /usr/bin/python3 -181: 39# _PyEval_EvalFrameDefault in /usr/bin/python3 -181: 40# 0x00000000004C3D1C in /usr/bin/python3 -181: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 -181: 42# _PyObject_Call_Prepend in /usr/bin/python3 -181: 43# 0x000000000052608C in /usr/bin/python3 -181: 44# _PyObject_MakeTpCall in /usr/bin/python3 -181: 45# _PyEval_EvalFrameDefault in /usr/bin/python3 -181: 46# 0x00000000004C3D1C in /usr/bin/python3 -181: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 -181: 48# _PyObject_Call_Prepend in /usr/bin/python3 -181: 49# 0x000000000052608C in /usr/bin/python3 -181: 50# _PyObject_MakeTpCall in /usr/bin/python3 -181: 51# _PyEval_EvalFrameDefault in /usr/bin/python3 -181: 52# _PyObject_Call_Prepend in /usr/bin/python3 -181: 53# 0x000000000051FB4C in /usr/bin/python3 -181: 54# 0x000000000051B324 in /usr/bin/python3 -181: 55# _PyObject_MakeTpCall in /usr/bin/python3 -181: 56# _PyEval_EvalFrameDefault in /usr/bin/python3 -181: 57# PyEval_EvalCode in /usr/bin/python3 -181: 58# 0x0000000000595200 in /usr/bin/python3 -181: 59# 0x00000000006757AC in /usr/bin/python3 -181: 60# _PyRun_SimpleFileObject in /usr/bin/python3 -181: 61# _PyRun_AnyFileObject in /usr/bin/python3 -181: 62# Py_RunMain in /usr/bin/python3 -181: 63# Py_BytesMain in /usr/bin/python3 -181: 64# 0x0000FFFF8F4B229C in /lib/aarch64-linux-gnu/libc.so.6 -181: 65# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -181: 66# _start in /usr/bin/python3 -181: ---------- -181: **** -181: -198/230 Test #195: pyTestThreads .......................... Passed 10.26 sec +198/230 Test #195: pyTestThreads .......................... Passed 16.82 sec test 210 Start 210: pyScaffoldNetwork 210: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/ScaffoldNetwork/Wrap/testScaffoldNetwork.py" 210: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap 210: Test timeout computed to be: 1500 -209: Randomness seeded to: 3543472329 +209: Randomness seeded to: 820151585 209: =============================================================================== 209: All tests passed (269 assertions in 19 test cases) 209: -199/230 Test #209: testScaffoldNetwork .................... Passed 3.38 sec +199/230 Test #209: testScaffoldNetwork .................... Passed 2.72 sec test 211 Start 211: pyScaffoldNetworkPickling @@ -34758,27 +34783,22 @@ 211: Test timeout computed to be: 1500 210: ....... 210: ---------------------------------------------------------------------- -210: Ran 7 tests in 0.181s +210: Ran 7 tests in 0.086s 210: 210: OK -208: Enumeration has completed -208: [02:23:47] Tautomer enumeration stopped at 86 tautomers: canceled -200/230 Test #210: pyScaffoldNetwork ...................... Passed 1.63 sec +200/230 Test #210: pyScaffoldNetwork ...................... Passed 1.03 sec test 212 Start 212: testMolEnumerator 212: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/testMolEnumerator 212: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator 212: Test timeout computed to be: 1500 -212: Randomness seeded to: 3016849774 -212: [02:23:47] can only enumerate SRUs with CONNECT=HT or CONNECT=HH -208: ..........[02:23:47] Explicit valence for atom # 1 N, 4, is greater than permitted -208: [02:23:47] Explicit valence for atom # 1 N, 4, is greater than permitted -208: [02:23:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +212: Randomness seeded to: 1388500270 +212: [23:11:14] can only enumerate SRUs with CONNECT=HT or CONNECT=HH 212: =============================================================================== 212: All tests passed (321 assertions in 16 test cases) 212: -201/230 Test #212: testMolEnumerator ...................... Passed 0.12 sec +201/230 Test #212: testMolEnumerator ...................... Passed 0.19 sec test 213 Start 213: pyMolEnumerator @@ -34787,25 +34807,24 @@ 213: Test timeout computed to be: 1500 211: . 211: ---------------------------------------------------------------------- -211: Ran 1 test in 0.033s +211: Ran 1 test in 0.036s 211: 211: OK -208: [02:23:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -202/230 Test #211: pyScaffoldNetworkPickling .............. Passed 0.82 sec +202/230 Test #211: pyScaffoldNetworkPickling .............. Passed 1.19 sec test 214 Start 214: testAbbreviations 214: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/testAbbreviations 214: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations 214: Test timeout computed to be: 1500 -214: Randomness seeded to: 674779513 -214: [02:23:47] SMARTS Parse Error: syntax error while parsing: *fail -214: [02:23:47] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' -214: [02:23:47] no suitable SubstanceGroups found +214: Randomness seeded to: 1571974486 +214: [23:11:14] SMARTS Parse Error: syntax error while parsing: *fail +214: [23:11:14] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' +214: [23:11:14] no suitable SubstanceGroups found 214: =============================================================================== 214: All tests passed (195 assertions in 12 test cases) 214: -203/230 Test #214: testAbbreviations ...................... Passed 0.08 sec +203/230 Test #214: testAbbreviations ...................... Passed 0.10 sec test 215 Start 215: pyAbbreviations @@ -34814,74 +34833,66 @@ 215: Test timeout computed to be: 1500 213: ... 213: ---------------------------------------------------------------------- -213: Ran 3 tests in 0.020s +213: Ran 3 tests in 0.036s 213: 213: OK -204/230 Test #213: pyMolEnumerator ........................ Passed 0.77 sec +215: ....... +215: ---------------------------------------------------------------------- +215: Ran 7 tests in 0.050s +215: +215: OK +204/230 Test #213: pyMolEnumerator ........................ Passed 1.29 sec test 216 Start 216: generalizedSubstructCatch 216: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/generalizedSubstructCatch 216: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct 216: Test timeout computed to be: 1500 -148: --------------------------------- -148: test getO3AForProbeConfs -148: -148: *********************************************************** -205/230 Test #148: testO3AAlign ........................... Passed 49.11 sec +208: Enumeration has completed +205/230 Test #215: pyAbbreviations ........................ Passed 0.98 sec test 217 Start 217: pyGeneralizedSubstruct 217: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/GeneralizedSubstruct/Wrap/testGeneralizedSubstruct.py" 217: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap 217: Test timeout computed to be: 1500 -215: ....... -215: ---------------------------------------------------------------------- -215: Ran 7 tests in 0.037s -215: -215: OK -145: [02:23:48] UFFTYPER: Unrecognized atom type: S_6+6 (0) -145: [02:23:48] UFFTYPER: Warning: hybridization set to SP3 for atom 0 -145: [02:23:48] UFFTYPER: Unrecognized charge state for atom: 0 -206/230 Test #215: pyAbbreviations ........................ Passed 0.93 sec +208: [23:11:15] Tautomer enumeration stopped at 33 tautomers: canceled +216: Randomness seeded to: 423769573 +216: =============================================================================== +216: All tests passed (486 assertions in 10 test cases) +216: +206/230 Test #216: generalizedSubstructCatch .............. Passed 0.56 sec test 218 Start 218: testMolProcessing 218: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/testMolProcessing 218: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing 218: Test timeout computed to be: 1500 -216: Randomness seeded to: 2853072494 -216: =============================================================================== -216: All tests passed (486 assertions in 10 test cases) -216: -207/230 Test #216: generalizedSubstructCatch .............. Passed 0.90 sec +208: ..........[23:11:16] Explicit valence for atom # 1 N, 4, is greater than permitted +208: [23:11:16] Explicit valence for atom # 1 N, 4, is greater than permitted +208: [23:11:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +208: [23:11:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +217: ....... +217: ---------------------------------------------------------------------- +217: Ran 7 tests in 0.395s +217: +217: OK +207/230 Test #217: pyGeneralizedSubstruct ................. Passed 1.40 sec test 219 Start 219: pyMolProcessing 219: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/GraphMol/MolProcessing/Wrap/testMolProcessing.py" 219: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/Wrap 219: Test timeout computed to be: 1500 -208: ............[02:23:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -208: [02:23:50] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. -208: [02:23:50] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. -217: ....... -217: ---------------------------------------------------------------------- -217: Ran 7 tests in 0.976s -217: -217: OK -208: ........[02:23:50] Explicit valence for atom # 1 O, 3, is greater than permitted -208: . -208: ---------------------------------------------------------------------- -208: Ran 37 tests in 7.634s -208: -208: OK -208: done +208: ............[23:11:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +208: [23:11:18] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. +208: [23:11:18] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. 219: .. 219: ---------------------------------------------------------------------- -219: Ran 2 tests in 0.409s +219: Ran 2 tests in 0.928s 219: 219: OK -208/230 Test #208: pyMolStandardize ....................... Passed 8.50 sec +208/230 Test #219: pyMolProcessing ........................ Passed 1.91 sec test 220 Start 220: testQuery @@ -34905,20 +34916,13 @@ 220: XOr 220: pointer and copy foo 220: Set2 -209/230 Test #219: pyMolProcessing ........................ Passed 1.86 sec -210/230 Test #220: testQuery .............................. Passed 0.02 sec +209/230 Test #220: testQuery .............................. Passed 0.08 sec test 221 Start 221: testMatCalc 221: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/testMatCalc 221: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc 221: Test timeout computed to be: 1500 -test 222 - Start 222: pyMatCalc - -222: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/DataManip/MetricMatrixCalc/Wrap/testMatricCalc.py" -222: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap -222: Test timeout computed to be: 1500 221: 1.68022e+08 221: 1.73149e+08 221: 1.05549e+08 @@ -34964,56 +34968,91 @@ 221: 9.49496e+07 221: 2.25618e+08 221: 1.30219e+08 -211/230 Test #221: testMatCalc ............................ Passed 0.06 sec +210/230 Test #221: testMatCalc ............................ Passed 0.03 sec +test 222 + Start 222: pyMatCalc + +222: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/DataManip/MetricMatrixCalc/Wrap/testMatricCalc.py" +222: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap +222: Test timeout computed to be: 1500 +208: ........[23:11:19] Explicit valence for atom # 1 O, 3, is greater than permitted +208: . +208: ---------------------------------------------------------------------- +208: Ran 37 tests in 7.922s +208: +208: OK +208: done +211/230 Test #208: pyMolStandardize ....................... Passed 9.01 sec test 223 Start 223: testSimDivPickers 223: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/SimDivPickers/testSimDivPickers 223: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/SimDivPickers 223: Test timeout computed to be: 1500 -223: [02:23:51] ------------------------------------- -223: [02:23:51] Testing github issue 1421: MaxMinPicker picking non-existent element. -223: [02:23:51] Done -223: [02:23:51] ------------------------------------- -223: [02:23:51] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. -223: [02:23:51] Done -212/230 Test #217: pyGeneralizedSubstruct ................. Passed 2.72 sec -213/230 Test #223: testSimDivPickers ...................... Passed 0.01 sec +223: [23:11:19] ------------------------------------- +223: [23:11:19] Testing github issue 1421: MaxMinPicker picking non-existent element. +223: [23:11:19] Done +223: [23:11:19] ------------------------------------- +223: [23:11:19] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. +223: [23:11:19] Done +212/230 Test #223: testSimDivPickers ...................... Passed 0.06 sec test 224 Start 224: pickersTestsCatch 224: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/SimDivPickers/pickersTestsCatch 224: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/SimDivPickers 224: Test timeout computed to be: 1500 +224: Randomness seeded to: 1838711788 +224: =============================================================================== +224: All tests passed (21267 assertions in 1 test case) +224: +213/230 Test #224: pickersTestsCatch ...................... Passed 0.46 sec test 225 Start 225: pySimDivPickers 225: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/SimDivPickers/Wrap/testPickers.py" 225: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/SimDivPickers/Wrap 225: Test timeout computed to be: 1500 -224: Randomness seeded to: 2820465854 -224: =============================================================================== -224: All tests passed (21267 assertions in 1 test case) -224: -214/230 Test #224: pickersTestsCatch ...................... Passed 0.26 sec +222: ..... +222: ---------------------------------------------------------------------- +222: Ran 5 tests in 0.897s +222: +222: OK +181: ............. +181: ---------------------------------------------------------------------- +181: Ran 19 tests in 39.267s +181: +181: OK +181: Testing atom rings +181: testing bond rings +181: searching atom rings +181: searching bond rings +181: done +214/230 Test #181: pySubstructLibrary ..................... Passed 40.59 sec test 226 Start 226: pyRanker 226: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/ML/InfoTheory/Wrap/testRanker.py" 226: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ML/InfoTheory/Wrap 226: Test timeout computed to be: 1500 -218: Randomness seeded to: 1212292203 -218: =============================================================================== -218: All tests passed (203 assertions in 1 test case) -218: -215/230 Test #218: testMolProcessing ...................... Passed 3.12 sec +215/230 Test #222: pyMatCalc .............................. Passed 1.78 sec test 227 Start 227: testChemicalFeatures 227: Test command: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ChemicalFeatures/testChemicalFeatures 227: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ChemicalFeatures 227: Test timeout computed to be: 1500 -226: ..[02:23:51] +227: ----------------------------------------- +227: Test1 +227: Done +216/230 Test #227: testChemicalFeatures ................... Passed 0.03 sec +test 228 + Start 228: pyFeatures + +228: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/ChemicalFeatures/Wrap/testFeatures.py" +228: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ChemicalFeatures/Wrap +228: Test timeout computed to be: 1500 +226: ..[23:11:20] 226: 226: **** 226: Invariant Violation @@ -35028,14 +35067,14 @@ 226: 3# RDInfoTheory::getTopNbits(RDInfoTheory::InfoBitRanker*, int) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so 226: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so 226: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -226: 6# 0x0000FFFF97B415C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +226: 6# 0x0000FFFF89DE15C0 in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 226: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 226: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 226: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 226: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 226: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/rdkit/rdBase.so 226: 12# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 -226: 13# 0x0000FFFF97B3E19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 +226: 13# 0x0000FFFF89DDE19C in /lib/aarch64-linux-gnu/libboost_python312.so.1.83.0 226: 14# _PyObject_MakeTpCall in /usr/bin/python3 226: 15# _PyEval_EvalFrameDefault in /usr/bin/python3 226: 16# 0x00000000004C3D1C in /usr/bin/python3 @@ -35068,7 +35107,7 @@ 226: 43# _PyRun_AnyFileObject in /usr/bin/python3 226: 44# Py_RunMain in /usr/bin/python3 226: 45# Py_BytesMain in /usr/bin/python3 -226: 46# 0x0000FFFF99F8229C in /lib/aarch64-linux-gnu/libc.so.6 +226: 46# 0x0000FFFF8C22229C in /lib/aarch64-linux-gnu/libc.so.6 226: 47# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 226: 48# _start in /usr/bin/python3 226: ---------- @@ -35076,61 +35115,43 @@ 226: 226: ... 226: ---------------------------------------------------------------------- -226: Ran 5 tests in 0.025s +226: Ran 5 tests in 0.048s 226: 226: OK -227: ----------------------------------------- -227: Test1 -227: Done -216/230 Test #227: testChemicalFeatures ................... Passed 0.04 sec -test 228 - Start 228: pyFeatures - -228: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.2/Code/ChemicalFeatures/Wrap/testFeatures.py" -228: Working Directory: /build/reproducible-path/rdkit-202409.2/obj-aarch64-linux-gnu/Code/ChemicalFeatures/Wrap -228: Test timeout computed to be: 1500 -217/230 Test #226: pyRanker ............................... Passed 0.66 sec +225: [23:11:20] the useCache argument is deprecated and ignored +217/230 Test #226: pyRanker ............................... Passed 0.46 sec test 229 Start 229: pythonProjectTests 229: Test command: /usr/bin/python3 "-m" "pytest" 229: Working Directory: /build/reproducible-path/rdkit-202409.2/Projects 229: Test timeout computed to be: 1500 -225: [02:23:51] the useCache argument is deprecated and ignored -222: ..... -222: ---------------------------------------------------------------------- -222: Ran 5 tests in 0.397s -222: -222: OK -218/230 Test #222: pyMatCalc .............................. Passed 1.15 sec +228: .. +228: ---------------------------------------------------------------------- +228: Ran 2 tests in 0.015s +228: +228: OK +228: Testing ChemicalFeatures Wrapper code: +225: ...[23:11:21] the useCache argument is deprecated and ignored +225: [23:11:21] the useCache argument is deprecated and ignored +225: .[23:11:21] the useCache argument is deprecated and ignored +218/230 Test #228: pyFeatures ............................. Passed 0.88 sec test 230 Start 230: pythonSourceTests 230: Test command: /usr/bin/python3 "-m" "pytest" 230: Working Directory: /build/reproducible-path/rdkit-202409.2/rdkit 230: Test timeout computed to be: 1500 -228: .. -228: ---------------------------------------------------------------------- -228: Ran 2 tests in 0.003s -228: -228: OK -228: Testing ChemicalFeatures Wrapper code: -219/230 Test #228: pyFeatures ............................. Passed 0.64 sec -225: ...[02:23:52] the useCache argument is deprecated and ignored -225: [02:23:52] the useCache argument is deprecated and ignored -225: .[02:23:52] the useCache argument is deprecated and ignored -229: ============================= test session starts ============================== -229: platform linux -- Python 3.12.8, pytest-8.3.4, pluggy-1.5.0 -229: rootdir: /build/reproducible-path/rdkit-202409.2/Projects -229: configfile: pytest.ini -229: plugins: typeguard-4.4.1 -229: collected 12 items -229: +218: Randomness seeded to: 1401076447 +218: =============================================================================== +218: All tests passed (203 assertions in 1 test case) +218: +219/230 Test #218: testMolProcessing ...................... Passed 6.15 sec 230: ImportError while loading conftest '/build/reproducible-path/rdkit-202409.2/rdkit/conftest.py'. 230: __init__.py:6: in 230: from . import rdBase 230: E ImportError: cannot import name 'rdBase' from partially initialized module 'rdkit' (most likely due to a circular import) (/build/reproducible-path/rdkit-202409.2/rdkit/__init__.py) -220/230 Test #230: pythonSourceTests ......................***Failed 1.37 sec +220/230 Test #230: pythonSourceTests ......................***Failed 0.82 sec ImportError while loading conftest '/build/reproducible-path/rdkit-202409.2/rdkit/conftest.py'. __init__.py:6: in from . import rdBase @@ -35138,49 +35159,45 @@ 225: ....... 225: ---------------------------------------------------------------------- -225: Ran 11 tests in 3.285s +225: Ran 11 tests in 2.085s 225: 225: OK -221/230 Test #225: pySimDivPickers ........................ Passed 4.17 sec -31: [02:23:59] Finished -31: [02:23:59] ------------------------------------- -31: [02:23:59] Test github1843: RWMol.clear() should not destroy ring pointer. -31: [02:23:59] Finished -31: [02:23:59] ------------------------------------- -31: [02:23:59] Test Github 6370: non-physical radical counts being preserved -31: [02:23:59] Finished -222/230 Test #31: graphmolTest1 .......................... Passed 73.89 sec -181: ............. -181: ---------------------------------------------------------------------- -181: Ran 19 tests in 39.732s -181: -181: OK -181: Testing atom rings -181: testing bond rings -181: searching atom rings -181: searching bond rings -181: done -223/230 Test #181: pySubstructLibrary ..................... Passed 41.04 sec -206: [02:24:06] Explicit valence for atom # 0 Br, 1, is greater than permitted +221/230 Test #225: pySimDivPickers ........................ Passed 3.30 sec +31: [23:11:25] Finished +31: [23:11:25] ------------------------------------- +31: [23:11:25] Test github1843: RWMol.clear() should not destroy ring pointer. +31: [23:11:25] Finished +31: [23:11:25] ------------------------------------- +31: [23:11:25] Test Github 6370: non-physical radical counts being preserved +31: [23:11:25] Finished +222/230 Test #31: graphmolTest1 .......................... Passed 115.03 sec +229: ============================= test session starts ============================== +229: platform linux -- Python 3.12.8, pytest-8.3.4, pluggy-1.5.0 +229: rootdir: /build/reproducible-path/rdkit-202409.2/Projects +229: configfile: pytest.ini +229: plugins: typeguard-4.4.1 +229: collected 12 items +229: +144: [23:11:43] done +206: [23:11:46] Explicit valence for atom # 0 Br, 1, is greater than permitted 206: =============================================================================== 206: All tests passed (38339 assertions in 50 test cases) 206: -224/230 Test #206: molStandardizeCatchTest ................ Passed 27.44 sec -144: [02:24:07] done -144: [02:24:07] --------------------------------- -144: [02:24:07] test github issue 256: handling of zero-atom molecules +223/230 Test #206: molStandardizeCatchTest ................ Passed 42.15 sec +144: [23:11:43] --------------------------------- +144: [23:11:43] test github issue 256: handling of zero-atom molecules 144: -144: [02:24:07] --------------------------------- -144: [02:24:07] test embedder callback function -144: [02:24:07] --------------------------------- -144: [02:24:07] test multi-threaded multi-conf embedding +144: [23:11:43] --------------------------------- +144: [23:11:43] test embedder callback function +144: [23:11:43] --------------------------------- +144: [23:11:43] test multi-threaded multi-conf embedding 144: -144: [02:24:10] --------------------------------- -144: [02:24:10] test github issue 563: Incorrect ring stereochemistry after embedding +144: [23:11:50] --------------------------------- +144: [23:11:50] test github issue 563: Incorrect ring stereochemistry after embedding 144: 144: CNC[C@H]1CC[C@H](C[NH3+])CC1 -144: [02:24:11] --------------------------------- -144: [02:24:11] test github issue 568: Incorrect stereochemistry after embedding +144: [23:11:53] --------------------------------- +144: [23:11:53] test github issue 568: Incorrect stereochemistry after embedding 144: 144: C1=NC[C@]2(CN3CC[C@@H]2C3)O1 144: O=C(O)[C@@H]1[C@H](C(=O)O)[C@H]2CC[C@@H]1O2 @@ -35193,18 +35210,22 @@ 144: CCCCC[C@H](O)/C=C/[C@@]1(F)[C@H](O)C[C@H](O)[C@@H]1C/C=C\CCCC(=O)OC 144: CCCCC[C@@H](O)/C=C/[C@@]1(F)[C@H](C/C=C\CCCC(=O)OC)[C@H](O)C[C@@H]1O 144: CNC(=O)Oc1cccc2c1OC[C@@H]1CCN(C)[C@H]21 +144: CNC(=O)Oc1ccc2c(c1)[C@@H]1[C@@H](CCN1C)CO2 +169: =============================================================================== +169: All tests passed (93 assertions in 5 test cases) +169: +224/230 Test #169: testRascalCluster ...................... Passed 110.13 sec 145: =============================================================================== 145: All tests passed (12735 assertions in 18 test cases) 145: -225/230 Test #145: distGeomHelpersCatch ................... Passed 78.33 sec -144: CNC(=O)Oc1ccc2c(c1)[C@@H]1[C@@H](CCN1C)CO2 +225/230 Test #145: distGeomHelpersCatch ................... Passed 129.14 sec 144: CN1CC[C@H]2COc3c(O)cccc3[C@H]21 144: CC(=O)C[C@@]12CCC[C@H]1[C@@H]1CCC3=CC(=O)CC[C@@H]3[C@H]1CC2 -169: =============================================================================== -169: All tests passed (93 assertions in 5 test cases) -169: -226/230 Test #169: testRascalCluster ...................... Passed 68.34 sec 144: O=C(O)[C@@H]1C[C@H]2C[C@@H](CCc3nn[nH]n3)CC[C@H]2CN1 +144: COc1ccc2c(c1)OC[C@@H](N1CCC(O)(c3ccc(F)cc3)CC1)[C@H]2O +144: Oc1ccc2c(c1)OC[C@@H](N1CCC(Cc3ccccc3)CC1)[C@H]2O +144: Oc1ccc2c(c1)OC[C@H](N1CCC(O)(c3ccccc3)CC1)[C@@H]2O +144: CC(=O)c1ccc2c(c1)[C@@]13CCCC[C@H]1[C@@H](C2)N(CC1CC1)CC3 229: DbCLI/UnitTestDbCLI.py ............ [100%] 229: 229: =============================== warnings summary =============================== @@ -35213,12 +35234,8 @@ 229: decBase = declarative_base() 229: 229: -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -229: ======================== 12 passed, 1 warning in 24.90s ======================== -144: COc1ccc2c(c1)OC[C@@H](N1CCC(O)(c3ccc(F)cc3)CC1)[C@H]2O -227/230 Test #229: pythonProjectTests ..................... Passed 25.57 sec -144: Oc1ccc2c(c1)OC[C@@H](N1CCC(Cc3ccccc3)CC1)[C@H]2O -144: Oc1ccc2c(c1)OC[C@H](N1CCC(O)(c3ccccc3)CC1)[C@@H]2O -144: CC(=O)c1ccc2c(c1)[C@@]13CCCC[C@H]1[C@@H](C2)N(CC1CC1)CC3 +229: ======================== 12 passed, 1 warning in 53.05s ======================== +226/230 Test #229: pythonProjectTests ..................... Passed 55.40 sec 144: CC(=O)O[C@@H]1CC[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C1)OCO5 144: COc1cc2c(cc1OC)[C@@H]1C[C@@H]3C[C@H](O)CC[C@@H]3CN1CC2 144: N#C[C@@H]1C[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C[C@@H]1O)OCO5 @@ -35228,53 +35245,74 @@ 144: C[C@H](C(N)=O)N1CC[C@@]23CCCC[C@@H]2[C@@H]1Cc1ccc(OCc2cccc(F)c2)cc13 144: CN1C(=O)CC[C@@]2(C)C1=CCc1cc(Cl)ccc12 144: Cc1nc(COc2ccc3c(c2)[C@@H](O)[C@@H](Cc2cccnc2)CO3)ccc1[N+](=O)[O-] +144: [23:12:41] Molecule does not have explicit Hs. Consider calling AddHs() +144: [23:12:28] --------------------------------- +144: [23:12:28] test github issue 696: Bad 1-4 bounds matrix elements in highly constrained system +144: [23:12:28] --------------------------------- +144: [23:12:28] More ChEMBL molecules failing bounds smoothing. +144: [23:12:28] --------------------------------- +144: [23:12:28] ugly conformations can be generated for highly constrained ring systems. +144: [23:12:28] --------------------------------- +144: [23:12:28] test embed parameters structure. +144: [23:12:28] --------------------------------- +144: [23:12:28] test github 1227: Hs being used in RMSD filtering. +144: [23:12:28] --------------------------------- +144: [23:12:28] Failure to embed larger aromatic rings. +144: [23:12:31] --------------------------------- +144: [23:12:31] Deterministic with large random seeds +144: [23:12:37] --------------------------------- +144: [23:12:37] Github #1990: seg fault after RemoveHs +144: [23:12:37] --------------------------------- +144: [23:12:37] Github #2246: Use coordMap when starting embedding from random coords +144: [23:12:41] --------------------------------- +144: [23:12:41] Providing a distance bounds matrix. +144: [23:12:41] --------------------------------- +144: [23:12:41] Disabling fragmentation. +144: [23:12:41] --------------------------------- +144: [23:12:41] Using symmetry in conformation pruning. +144: [23:12:41] --------------------------------- +144: [23:12:41] Force trans amides. +144: [23:12:41] --------------------------------- +144: [23:12:41] test missing Hs warning. +144: [23:12:41] --------------------------------- +144: [23:12:41] basic H bond support. +144: [23:12:41] ******************************************************* +227/230 Test #144: testDistGeomHelpers .................... Passed 166.19 sec 168: =============================================================================== 168: All tests passed (2923 assertions in 27 test cases) 168: -228/230 Test #168: testRascalMCES ......................... Passed 76.14 sec -144: [02:24:27] Molecule does not have explicit Hs. Consider calling AddHs() -144: [02:24:23] --------------------------------- -144: [02:24:23] test github issue 696: Bad 1-4 bounds matrix elements in highly constrained system -144: [02:24:23] --------------------------------- -144: [02:24:23] More ChEMBL molecules failing bounds smoothing. -144: [02:24:23] --------------------------------- -144: [02:24:23] ugly conformations can be generated for highly constrained ring systems. -144: [02:24:23] --------------------------------- -144: [02:24:23] test embed parameters structure. -144: [02:24:23] --------------------------------- -144: [02:24:23] test github 1227: Hs being used in RMSD filtering. -144: [02:24:23] --------------------------------- -144: [02:24:23] Failure to embed larger aromatic rings. -144: [02:24:25] --------------------------------- -144: [02:24:25] Deterministic with large random seeds -144: [02:24:26] --------------------------------- -144: [02:24:26] Github #1990: seg fault after RemoveHs -144: [02:24:26] --------------------------------- -144: [02:24:26] Github #2246: Use coordMap when starting embedding from random coords -144: [02:24:27] --------------------------------- -144: [02:24:27] Providing a distance bounds matrix. -144: [02:24:27] --------------------------------- -144: [02:24:27] Disabling fragmentation. -144: [02:24:27] --------------------------------- -144: [02:24:27] Using symmetry in conformation pruning. -144: [02:24:27] --------------------------------- -144: [02:24:27] Force trans amides. -144: [02:24:27] --------------------------------- -144: [02:24:27] test missing Hs warning. -144: [02:24:27] --------------------------------- -144: [02:24:27] basic H bond support. -144: [02:24:27] ******************************************************* -229/230 Test #144: testDistGeomHelpers .................... Passed 90.20 sec -5: [02:30:02] Finished: testMultipleTimes() -5: [02:30:02] -5: ----------------------------------------- -230/230 Test #5: testConcurrentQueue .................... Passed 437.28 sec +228/230 Test #168: testRascalMCES ......................... Passed 152.46 sec +229/230 Test #5: testConcurrentQueue ....................***Timeout 1500.01 sec +[23:09:28] +----------------------------------------- +[23:09:29] Finished: testPushAndPop() +[23:09:29] +----------------------------------------- +[23:09:29] +----------------------------------------- + +230/230 Test #72: testGeneralFileReader ..................***Timeout 1500.04 sec +[23:09:34] +----------------------------------------- +[23:09:34] Finished: testDetermineFormat() +[23:09:34] ----------------------------------------- + +[23:09:34] +----------------------------------------- +[23:09:34] Finished: testSdf() +[23:09:34] ----------------------------------------- + +[23:09:34] +----------------------------------------- + -99% tests passed, 1 tests failed out of 230 +99% tests passed, 3 tests failed out of 230 -Total Test time (real) = 437.34 sec +Total Test time (real) = 1506.58 sec The following tests FAILED: + 5 - testConcurrentQueue (Timeout) + 72 - testGeneralFileReader (Timeout) 230 - pythonSourceTests (Failed) Errors while running CTest make[2]: *** [Makefile:94: test] Error 8 @@ -37877,44 +37915,44 @@ diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged -dpkg-shlibdeps: warning: symbol PyObject_CallFunction used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries -dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries +dpkg-shlibdeps: warning: debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/rdkit.so contains an unresolvable reference to symbol pg_snprintf: it's probably a plugin +dpkg-shlibdeps: warning: 24 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol PyExc_KeyError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyExc_RuntimeError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyExc_ValueError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_SetObject used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries -dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyObject_IsTrue used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyExc_RuntimeError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyObject_CallFunction used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.2 found in none of the libraries dpkg-shlibdeps: warning: 2 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/rdkit.so contains an unresolvable reference to symbol byteain: it's probably a plugin -dpkg-shlibdeps: warning: 24 other similar warnings have been skipped (use -v to see them all) dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake +dpkg-gencontrol: warning: Depends field of package librdkit-dev: substitution variable ${shlibs:Depends} used, but is not defined +dpkg-gencontrol: warning: package librdkit-dev: substitution variable ${python3:Depends} unused, but is defined +dpkg-gencontrol: warning: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined dpkg-gencontrol: warning: Depends field of package rdkit-data: substitution variable ${shlibs:Depends} used, but is not defined +dpkg-gencontrol: warning: package rdkit-data: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: Depends field of package rdkit-doc: substitution variable ${shlibs:Depends} used, but is not defined -dpkg-gencontrol: warning: Depends field of package librdkit-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package postgresql-17-rdkit: substitution variable ${python3:Depends} unused, but is defined -dpkg-gencontrol: warning: package rdkit-data: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package librdkit1t64: substitution variable ${python3:Depends} unused, but is defined -dpkg-gencontrol: warning: package librdkit-dev: substitution variable ${python3:Depends} unused, but is defined -dpkg-gencontrol: warning: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined dpkg-gencontrol: warning: package rdkit-doc: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package postgresql-17-rdkit: substitution variable ${python3:Depends} unused, but is defined -dpkg-gencontrol: warning: package librdkit1t64: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined +dpkg-gencontrol: warning: package librdkit1t64: substitution variable ${python3:Depends} unused, but is defined dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_202409.2-2_all.deb'. dpkg-deb: building package 'librdkit1t64-dbgsym' in '../librdkit1t64-dbgsym_202409.2-2_arm64.deb'. +dpkg-deb: building package 'python3-rdkit' in '../python3-rdkit_202409.2-2_arm64.deb'. +dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202409.2-2_arm64.deb'. +dpkg-deb: building package 'postgresql-17-rdkit' in '../postgresql-17-rdkit_202409.2-2_arm64.deb'. dpkg-deb: building package 'rdkit-data' in '../rdkit-data_202409.2-2_all.deb'. dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202409.2-2_arm64.deb'. -dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202409.2-2_arm64.deb'. dpkg-deb: building package 'librdkit1t64' in '../librdkit1t64_202409.2-2_arm64.deb'. -dpkg-deb: building package 'python3-rdkit' in '../python3-rdkit_202409.2-2_arm64.deb'. dpkg-deb: building package 'postgresql-17-rdkit-dbgsym' in '../postgresql-17-rdkit-dbgsym_202409.2-2_arm64.deb'. -dpkg-deb: building package 'postgresql-17-rdkit' in '../postgresql-17-rdkit_202409.2-2_arm64.deb'. dpkg-genbuildinfo --build=binary -O../rdkit_202409.2-2_arm64.buildinfo dpkg-genchanges --build=binary -O../rdkit_202409.2-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -37922,12 +37960,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/327883/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/327883/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/2847219 and its subdirectories -I: Current time: Tue Jan 20 02:32:38 -12 2026 -I: pbuilder-time-stamp: 1768919558 +I: removing directory /srv/workspace/pbuilder/327883 and its subdirectories +I: Current time: Wed Dec 18 23:42:11 +14 2024 +I: pbuilder-time-stamp: 1734514931